Space Plague
by karkovice
Summary: This is the sequel to "The Visitors". Just four months after the crew of the Enterprise left Equestria, Rarity comes down with an unknown disease! Captain Kirk and his crew are summoned back to Equestria to try to find the cure for the mysterious disease that's afflicted Rarity, and prevent a planet wide epidemic. Meanwhile, a familiar villain plots to take over Equestria!
1. Chapter 1 - Illness

**SPACE PLAGUE**

**A MY LITTLE PONY: FRIENDSHIP IS MAGIC/**

**ORIGINAL STAR TREK SERIES CROSSOVER STORY**

**CHAPTER 1**

**ILLNESS**

It was a bright, sunny day in Ponyville! The temperature was quite mild. It was summerlike weather, even though it was the beginning of fall. The trees all around were still lush and green, but the leaves would soon be changing colour. That means it would almost be time for the annual Running Of The Leaves race!

In the park outside the village, a group of ponies were having a picnic! But this wasn't just any ordinary group of ponies; these were the _wielders of the Elements of Harmony _themselves! First, there was Fluttershy, who wielded the Element of Kindness. She was an unassuming yellow coloured Pegasus female with light pink mane and tail who mostly kept to herself, and often times spoke in a barely audible voice, hence her shy nature. Then there was Rainbow Dash, her fellow Pegasus compatriot, dear friend, and wielder of the Element of Loyalty. She was a very boastful light blue coloured mare who wasn't afraid to call herself "Awesome!" every chance she got. The most striking feature with her was her rainbow coloured mane and tail, and she was known to perform an aerial feat known to the locals as the "Sonic Rainboom" every now and then. Then there was Pinkie Pie, the wielder of the Element of Laughter. She was a fun loving pink coloured Earth pony who really liked to throw parties and make everypony happy.

Then there was the leader of the group, Twilight Sparkle, who was the wielder of the Element of Magic. She was born a purple coloured unicorn pony with dark blue coloured mane and tail with pink and light purple highlights. She was wielder of the Element of Magic because she had a singular gift for unicorn magic and complicated spells, and she proved that fact many times over!

Recently, though, she underwent a transformation where she suddenly sprouted Pegasus wings! This was the aftermath of a very important test imposed upon her by Princess Celestia, a tall and beautiful bright white coloured alicorn who was the ruler of all of Equestria; who also acted as teacher and mentor to the gifted Twilight Sparkle. The test involved her completing a long forgotten powerful spell started by Starswirl the Bearded, a powerful unicorn mage from the days of old.

Against all odds, Twilight Sparkle was able to complete the spell; and as such, Princess Celestia transformed her into an _alicorn. _It was only a short time later that the new alicorn Twilight was crowned a _Princess. _A short time after _that, _she moved back to Canterlot to begin her training in mastering her newly acquired alicorn powers. Princess Celestia looked after that personally. Not only _that, _but she also had to get lessons in proper etiquette, as she was also a _Princess _now, and had to behave as such! Princess Celestia looked after that as well. Princess Luna, the dark blue coloured alicorn Princess of The Night, and Celestia's younger sister, helped every now and then in that area.

When Twilight Sparkle left for Canterlot, she left the Ponyville Library, her former home, in the care of Spike; a diminutive purple dragon who acted as her faithful assistant for years. He was also Twilight Sparkle's dear friend, and he helped her overcome many obstacles throughout her life.

There was talk of actually converting the Ponyville Library into a Palace, and making Twilight Sparkle Princess of Ponyville, but nothing was finalized yet. Yet despite her busy schedule, Twilight Sparkle still found the time to visit her friends in Ponyville once a week. On this day, they all decided to have a picnic!

They were waiting for two other ponies to arrive, though. One was Applejack, an orange coloured Earth pony mare with blonde mane and tail who worked on an apple farm called Sweet Apple Acres. She spent long hours bucking apples from the many trees of the farm's expansive apple orchards. She was also the wielder of the Element of Honesty, because she always told the truth and was very trustworthy.

The other was Rarity, a white coloured unicorn mare with highly stylized dark blue mane and tail. She worked as a Seamstress and Fashion Designer in Ponyville, and owned a shop just outside of the town square. She often thought of herself as being high classed, and was prone to having phases of extreme vanity. She also often acted out as the over reactive _drama queen, _which sometimes drove her friends _nuts! _Yet despite these flaws, she was the perfect pony to wield the Element of Generosity, because she always gave herself and her time to anypony who needed it without a second thought!

"What a super duper luper fantastic DAY to have a PICNIC!" Pinkie Pie said, happily bouncing around, like she always does.

"You _said _it!" said Rainbow Dash, who was lying on the picnic blanket with her forelegs tucked behind her head and her rear legs crossed in a relaxed position. She was also wearing her sunglasses!

"When are Applejack and Rarity gonna get here?" asked the soft spoken Fluttershy.

"They should be here any minute _now."_ Twilight Sparkle said. "They wouldn't miss this for _anything!"_

No sooner had she said that that the familiar orange coloured Earth pony mare appeared into view.

"Hi, Applejack!"all of the girls said in unison once they saw her approach.

"Hey y'all!" Applejack said in her Southern accent. There was a lot of sadness in her voice. She also looked quite sad.

Twilight Sparkle was the first to notice this. "What's wrong?" she asked in a worried tone.

"Where's Rarity?" Fluttershy asked with one forehoof upraised.

Applejack sighed. "Rarity ain't comin'…"

"Not _coming!?" _Pinkie Pie exclaimed with a gasp as she pressed her two forehooves to her cheeks. "Why _not!?"_

"Ah just dropped 'er off at the hospital… She's _ill!"_

A collective gasp rose up from the group at this shocking news.

* * *

_My little pony! My little pony! AAH AAH AAH AAH!_

_My little pony! I used to wonder what friendship could be(my little pony)_

'_Til you all shared its magic with me!_

_Big adventure_

_Tons of fun_

_A beautiful heart_

_Faithful and strong_

_Sharing kindness, it's an easy feat_

_And magic makes it all complete, YES!_

_My little pony! Do you know you are my very best friends!?_

* * *

The mares just stood in stunned silence at the news Applejack just gave them.

Moments later, Rainbow Dash broke the silence by crying out "What do you mean 'she's ill'!? I saw her yesterday, and she seemed fine to me!"

"All ah know is" Applejack began. "When she woke up this mornin', she was feelin' quite _under the weather. _When ah went to her house ta pick 'er up, she looked quite _tired, _an' said that she was sufferin' from aches and pains. She asked me to take 'er to the _hospital _thinkin' it maght be a case o' the _flu."_

Everypony looked sad at the notion that their friend was sick in the hospital.

"Well, what do you think we should _do?" _Fluttershy asked after a few moments.

"Well, we should at least go _see _her!" Twilight Sparkle answered with finality. "She's our _friend _who's been through thick and thin with us all the way! We owe her _that _much, at least."

"I agree completely!" Pinkie Pie said.

"Me, too!" Rainbow dash said. "Okay, Twi, lead the way."

With this, they dropped the picnic and hurried in the direction of Ponyville Hospital, where their long time friend Rarity was hospitalized.

* * *

It didn't take them very long to reach Ponyville Hospital. They rushed in looking for where Rarity might be hospitalized. They were met by Nurse Redheart, who was dressed in full surgical gear.

"Nurse Redheart!" Twilight Sparkle said in greeting.

Nurse Redheart gasped slightly upon seeing her. "Princess Twilight Sparkle!" she said and immediately began to bow.

Twilight Sparkle stopped her by placing her forehooves on her shoulders. Nurse Redheart looked up, slightly startled.

"No formalities!" Twilight Sparkle said. "We're here to see _Rarity!"_

"Oh! Right…" Nurse Redheart said. "I figured you girls'd show up _sooner or later. _Follow me!"

She led them to an area of the hospital that was the Intensive Care Unit. She stopped in front of a bay window and gestured for Twilight Sparkle and her friends to look inside. What they saw stunned them all! They saw Rarity lying in a hospital bed hooked up to a respirator. There was a I.V. implanted in her left foreleg, and she looked ten years older than she really was! A male Earth pony Doctor was tending to her. Standing by the door to the room were two male unicorn Nurses. They were all dressed in full protective surgical gear. The threshold of the door that led into the room was curtained off, and the curtaining was extended to a few feet beyond the door. The male Nurses were standing guard. It looked like a Medical Quarantine!

This was confirmed when Nurse Redheart spoke again. "We've got her under Quarantine! I must admit, I've never seen anything _like _this! She's got all of the symptoms of a severe flu, but I think it's _more_ than the flu!"

"Well, what's she come down with?" Twilight Sparkle asked.

"That's just _it!" _Nurse Redheart admitted. "We don't know _what _she's got! Even Doctor Heartthrob's baffled!"

"She looks _really bad_, Twilight!" Fluttershy cried as she laid a forehoof on Twilight's shoulder. "I'm _worried _for her!"

"We _all _are, Fluttershy!" Twilight said as she laid a comforting hoof on Fluttershy's shoulders.

"We gotta do _something!" _Rainbow Dash exclaimed.

"What do ya _suggest?" _Applejack asked.

"Well, for starters, we should go in there and-" Rainbow Dash began as she moved to enter the room.

"NO!" Nurse Redheart exclaimed as she stopped Rainbow Dash before the threshold. "Not unless you wanna risk getting infected _yourselves!"_

"Well, we can't just _stand _here!" Rainbow Dash said in despair.

"Ah agree!" Applejack said. "We gotta at least _try _to do _somethin'_, y'all!"

"Applejack's right!" Pinkie Pie said. "I just can't _stand _to see her LOOKING like this!" She looked quite sad, almost to the point of tears.

"Hmmm…" Twilight Sparkle became pensive as she brought a forehoof to her chin. "I _must _contact Princess Celestia!" she finally said. "SHE'LL know what do to! And for _that, _I'll need Spike. You girls stay here! I'll be back as soon as I can!"

With this, she galloped off in the direction of the Ponyville Library where she was sure to find Spike.

* * *

In the Throne Room of Canterlot Palace, Princess Celestia, the official ruler of Equestria, was busy pouring over some official documents. She stood six and a half feet tall- seven foot four, if you included her alicorn's horn – and had a pure white coat with a sun symbol cutie mark, thus denoting her as the Sun Princess capable of raising and lowering the sun at will, thanks to her awesome alicorn powers. She had a multicoloured mane and tail that flowed constantly, as if by magic.

Her official business was interrupted by a green flash a few feet away from her. Out of that flash came a rolled up parchment that fell to the floor. She used her alicorn magic to pick the parchment up. She knew instantly who it was from just by looking at it! _It's from Princess Twilight Sparkle. What does she want? _She thought to herself.

She used her magic to unroll the parchment. She read the following:

_Dear Princess Celestia,_

_I apologize in advance for disturbing you at this time of the day, but a crisis has arisen in Ponyville!_

_Rarity, my good friend and wielder of the Element of Generosity, has taken ill with an unknown disease! She is currently being looked after at the Ponyville Hospital with severe flulike symptoms, but the Doctors keep insisting that it's not the flu! Matter of fact, they are totally at a loss as to what's causing her ailment!_

_Can you please advise?_

_Princess Twilight Sparkle_

After reading the letter to her by her long time loyal and faithful student, Princess Celestia became pensive. The look on her facial features betrayed worry. She cared very deeply for all of her subjects, and frequently took it upon herself to guarantee their safety and well being. The news of one of the wielders of the Elements of Harmony, the literal guardians of Equestria, taking ill suddenly, was _most_ distressful!

Out of a side door next to the Royal Throne, another alicorn figure appeared. This alicorn was smaller than Celestia, standing only 5 feet tall – five foot nine, if you included her horn – and was dark blue in colour. Her cutie mark was a white crescent moon overlayed against a pitch black sky, thus denoting her as the Moon Princess. Her flowing mane and tail were of a lighter blue shade, and seemed to carry twinkling stars. This was Princess Luna, the Princess of The Night!

"Sister?" she said as she approached her elder sibling.

Celestia was startled slightly by the sound of her younger sister's voice. "Oh! Luna…" she said as she turned a glance at her sibling. "I didn't hear you come in…"

Luna noticed that her sister was not her usual joyous self. "What is wrong, dear sister?" she asked. "You seem… troubled…"

"I just received word from Princess Twilight Sparkle that one of the wielders of the Elements of Harmony has come down with an unknown disease…"

"Unknown disease?" Luna asked.

"Yes…" Celestia said as she handed the parchment to her younger sister to read.

As Luna read the parchment, her eyebrows lifted momentarily, thus betraying an emotion of surprise. It looked familiar to Celestia somehow. "This is most disturbing _indeed!" _Luna said as she lowered the parchment. "Any idea what could be causing this ailment?"

Princess Celestia looked up at a familiar stained glass window to her left. "No…But I think I know who'd might. Excuse me…" she said as she got up from the Throne and proceeded towards the side door that lead out of the Throne Room.

Princess Luna moved to follow her elder sister. "Your Highness!" came a voice from her left that made her stop. It belonged to the member of the Royal Guard who directed traffic in and out of the Throne Room. This male Earth pony was dark yellow in colour with a two toned blue mane and tail. He also wore the polished gold coloured uniform of the Palace Guards. "Sorry to disturb you," he began as he trotted up to stand a few feet away from the Throne. "but there are subjects in the hall outside who wish to have an audience."

"How many?" Luna asked.

The male pony looked nervous. "_Several, _Your Highness…"

Luna glanced over towards the Throne that was just abandoned by her elder sister. She took it upon herself to take her place on it.

"Thou art new here?" Princess Luna casually asked.

The male pony nodded. "Y-yes, Your Highness. I joined the Royal Guard barely two months ago."

"What is thy name?"

The male pony swallowed nervously. "F-Flash Sentry, Your Highness…"

Princess Luna smiled. "Well, I welcome thee to our service, Flash Sentry!"

Flash Sentry relaxed a bit and bowed slightly, smiling. "Thank you, Your Highness!"

"You may send the first ones in…" Princess Luna ordered.

"_Yes, _Your Highness!" Flash Sentry bowed, then trotted back to the large double doors at the end of the Throne Room let in the first of Equestria's Loyal Subjects who wish to see Equestrian Royalty.


	2. Chapter 2 - Mission's End

**CHAPTER 2**

**MISSION'S END**

_Captain's Log, Star Date 5192.3 – After four months of exploring the Pegasus constellation, we are finally nearing the end of our mission. We have assumed orbit around the third planet orbiting the star we have named "Equus Minor", a star very much like our own Sun. The planet itself is very much like our Earth, with abundant vegetation and lower animal life forms; but no detectable civilizations. _

_Once our mission is complete, we are due to report to Star Base 9 where most of us will go on a well deserved two months of shore leave._

The turbo lift doors leading to the Bridge swished open to reveal Mr. Spock, the Vulcan Commander of the Enterprise. He immediately went to stand next to Captain James T. Kirk, who was seated in his Captain's chair. He had just handed the Log Recorder back to Yeoman Rand as the Vulcan came beside him.

"The last geological survey teams have beamed down to the planet." Spock reported as he crossed his hands behind his back. "In twelve hours, they are to report back to the Enterprise; where we will then be ready to leave orbit."

"Very good, Mr. Spock!" Kirk said in response. "I must say that this mission had been a _huge success, _wouldn't you say?"

"Indeed!" Spock said. "The vast amounts of information we have gathered on the planets we've explored should keep Starfleet and the Vulcan Science Academy busy for quite some time."

"But I'm sure that, without a doubt, the most _extraordinary _world we've explored was the one inhabited by the sentient ponies. What was it called?"

"Equus Major 4." Spock said in reply.

"But I think the local inhabitants called it _Equestria…" _Dr. Leonard McCoy, the Chief Medical Officer, who happened to be on the Bridge, said as he was listening in on the conversation.

"Ah, yes! _Equestria!" _Kirk smiled. "Quite a _magical _place…"

"It certainly was!" McCoy said, smiling himself.

Spock simply raised his eyebrows.

"Well, if there's nothing else, I'll retire to my quarters! Mr. Spock, you have the 'Con." Kirk said as he got up out of the Captain's chair.

"Yes, Captain." Spock said as he moved to take his place in the chair.

The turbo lift doors swooshed open just as Spock sat down. They swooshed closed behind Kirk as he walked in.

* * *

In his quarters, Captain Kirk was getting ready for bed. He was wearing his silk pajamas that were the same yellow colour as the shirt of his Starfleet uniform.

He casually glanced at the free standing mirror he kept in his quarters. This was not supposed to be any ordinary mirror, however; it was an alleged _magic _mirror given to him my Princess Celestia, the monarch ruler of Equestria. She told him that it allowed her to communicate with him, no matter where he was in the galaxy, and vice versa. Kirk never really believed it to be true. He always thought that it was just an embellished story meant to ensure that he wouldn't simply give the mirror away. He chuckled lightly as he admired his own reflection. He certainly did look _handsome!_ The many women he has had throughout his life could certainly testify to _that!_

He turned the lights out and climbed into bed. As soon as he settled down, his quarters were filled with a strange blue glowing light. The strange glowing light made him jump up! It wasn't long before he noticed that the light was coming from the free standing mirror, and it was bright enough to light his entire quarters with its eerie glow!

He got up and slowly approached the mirror. When he looked at it, he didn't see his own reflection! Instead, he saw a swirling sky filled with black clouds with several lightning bolts that emitted an eerie crackling sound! He also heard a strange humming sound, as if the clouded sky he saw was filled with some sort of strange power!

This persisted for about thirty seconds, then the swirling clouded sky winked out, the humming sound stopped and the light disappeared, plunging Kirk's quarters into darkness once more. Kirk just stood there dumbfounded by what he'd just seen and heard for a few seconds! Without a second thought, he moved back to his bed and crawled into it. He would soon drift off to sleep.

* * *

The next morning, Kirk made his way to Recreation Room 4, which was located on the same deck as his quarters were. He made his way to one of the Replicators and programmed it to give him a simple breakfast of coffee, bran cereal and toast. The Replicator warbled as it prepared his meal. It made a light dinging sound as the small door opened to reveal a tray containing his food. Many of the crew complained about the replicated food, which was mostly made up of reconstituted proteins, vitamins and minerals. They said that it didn't taste as great as _real _food. Kirk didn't notice any difference, perhaps it was because he had gotten so used to it.

The doors to the Recreation Room swished open to reveal Dr. McCoy, who made straight for the Replicators to manufacture his own breakfast. He picked up his tray from the Replicator compartment and went to join Kirk at his table.

"Morning, Jim!" the Doctor said happily.

"Bones…" Kirk said in reply as he took a sip from his coffee.

As Dr. McCoy sat down, he noticed something in his friend's mood. "What's wrong?" he asked.

"What!?" Kirk asked somewhat confused.

"I know you too well, Jim! I can tell when something's bothering you. You've not been having any bad dreams, have you?"

Kirk chuckled. "No, nothing like that… except…" He trailed off.

"Except _what!?" _McCoy pressed.

Kirk laughed. "Well, there was this _one _dream… if it _was, _in fact, a dream where…"

"Go on!" McCoy urged.

"You know that large free standing mirror I have in my quarters?"

"You mean the one Princess Celestia gave you, the supposed _magic _mirror?"

"_That's _the one! For some odd reason, it was doing something _strange _last night…"

McCoy looked worried. "What did it _do?"_

"It suddenly started _glowing _with an _eerie blue light, _bright enough to fill my entire quarters! Then, when I looked into it, instead of seeing my own reflection, I saw… _clouds _and… _lightning!"_

McCoy raised his eyebrow in puzzlement. "Well, you're _right, _that _is _a strange dream… Let me know if it happens again, all right?"

"Sure thing, Bones…"

They both continued on with their breakfast in silence.

* * *

The turbo lift doors to the Bridge swished open to reveal Captain Kirk, who quickly made his way to the Captain's chair. Mr. Spock immediately got up from his Science Station to go stand by Kirk's side. "The last geological survey teams have just beamed aboard. We are now ready to leave orbit." He announced.

"Very good, Mr. Spock! Mr. Chehkov, plot a course for Star Base 9!" Kirk ordered.

"Star Base 9, aye sair!" said a smiling Chekhov as he pressed the appropriate buttons on his Navigation console.

"Warp Factor 3!" Kirk ordered.

"Warp Factor 3, aye!" said Mr. Sulu from his Tactical Station as he pressed the appropriate buttons on his own console. "Course laid in, sir." Sulu announced.

"Engage!" Kirk announced.

Sulu pressed one more button, and you could hear the hum of the Warp Drive as it went into action causing the Enterprise to break orbit from the planet and make a heading for Star Base 9.

"ETA, Mr. Sulu?" Kirk asked.

"ETA seventy two point three hours, present speed!" Sulu said in response.

"Excellent!" said a smiling Captain Kirk, already looking forward to his much anticipated shore leave.

* * *

The rest of the day was uneventful for the crew of the Enterprise. Those who were slated to go on shore leave were already preparing for their much deserved vacation, while those who were to be reassigned were already preparing for their next assignment.

At the end of the day, Captain Kirk was in his quarters preparing for bed. He felt that he would sleep easy tonight after getting quite the workout in the ship's Gymnasium earlier that day! He wore the same yellow coloured silk pajamas he wore the night before. When he was ready, he turned the lights of his quarters off and immediately crawled into bed.

No sooner had he settled down that his quarters were suddenly filled with same eerie blue glow that was present the night before. This time, he didn't react so quickly. He slowly got up and looked in the direction of his free standing mirror. He was not at all surprised to see that the blue glow was emanating from the mirror, same as the night before!

Only this time, it was different! Instead of the crackling sound of lightning, he thought he heard a voice calling his name through the hum of power.

"Captain Kirk?" he heard the voice call again. This made him immediately get up out of bed.

"Captain James T. Kirk, are you there?" said the voice. It sounded familiar to Kirk, but he couldn't quite place it.

He slowly approached the mirror and dared himself to look at it. When he saw what was reflected back at him, he instantly knew why that voice sounded so familiar to him.

"Princess Celestia?" he said in surprise.

"_Yes, _Captain!" said a smiling Celestia from the mirror. "It is I, the Princess of all Equestria…"

Kirk laughed. "You know, I never really believed that this mirror actually _worked…"_

Celestia smiled again. "Me talking to you _now _is proof that it _does…"_

"Was it… _you _that tried to contact me last night!?"

Celestia nodded. "It _was! _My alicorn powers were not as strong as they are _now. _I've had a rather difficult day…"

Kirk chuckled. "Don't we all? SO, what do I owe the _pleasure?"_

Celestia became more serious. "I wish the circumstances were _better! _One of my dear subjects - a unicorn mare you have become quite acquainted to, I believe – has taken ill with an unknown disease…"

"You mean _Rarity?"_

Celestia nodded. "That's her! I somehow feel that _you _were the _involuntary_ _cause _of this…"

Kirk was dumbfounded. "_Me? _You mean… ME or someone from my _crew?"_

"Exactly! It is _imperative _that you come to our aid before more of my loyal subjects become _sick!" _

Kirk thought about it for a few moments, then finally nodded. "All right!" He then smiled. "You're lucky that we've just completed our exploration mission; otherwise, Starfleet would _never _have allowed this…"

Celestia smiled back. "Then it is _fortunate _that I have contacted you at the _right time… _Contact me when you arrive…"

Princess Celestia's image then faded from the mirror and Captain Kirk's quarters were plunged into darkness once again. Kirk then decided to immediately go to bed and try to get some sleep. He wasn't going to order the new heading tonight, seeing as Equestria was en route to Star Base 9. All that was required was a small detour that wouldn't put them out of their way too much. Kirk finally fell into an uneasy sleep as he was left wondering if someone from his crew really _did _infect the lovely and charming Rarity with a disease not native to the planet Equestria.

* * *

The next morning, Kirk made his way straight for the Bridge, not bothering to stop in the Recreation Room for breakfast. He was too preoccupied with what happened the night before to feel hungry enough to eat anything.

As soon as the turbo lift doors to the Bridge swished open, he made his way straight for the Captain's chair without a moment's hesitation.

"Mr. Chekhov, plot a new course heading one eight seven mark four!" Kirk ordered.

Mr. Spock turned from his Science Station to look questioningly at his Captain and long time friend.

Chekhov turned to face his Captain once he realized where the coordinates would take them. "But _sair, _that heading puts us straight for… Equus Major 4… more prwecisely… _Equestria…"_

"Why on Earth would we go there _again!?" _Mr. Sulu asked from his Tactical Station.

"I'll explain on the way…" Kirk said in response. "Just do as I say!"

Chekhov hesitated for a few moments. "Aye, sair!" he finally said. "Heading one eight seven mark _four…" _he said as he pressed the appropriate buttons on his console.

"Warp Factor 7!" Kirk ordered.

"Warp Factor 7, aye!" Mr. Sulu said as he pressed the appropriate buttons on his own console.

"Engage!" Kirk ordered.

"Aye, sir!" Sulu said as he pressed one more button on his console.

The hum of the warp drive resonated as the Enterprise diverted towards its new heading.

"What's out ETA?" Kirk asked.

"Six and a half hours at present velocity!" Sulu said in reply.

"I am most curious to hear your explanation for this…" Spock said as he moved to stand next to his Captain.

"And you'll _get it, _Mr. Spock!" Kirk said. "Just call Yeoman Rand up here, and tell her to bring the Log Recorder with her…"

"Yes, Captain." Spock said before moving to his Science Station to carry out Kirk's order.

_Captain's Log, Star Date 5192.6 – After being contacted by Princess Celestia of Equestria via the magic mirror she gave me, I have diverted the Enterprise on a new heading towards that planet. She brought news of a crisis where one of her subjects has taken ill with an unknown disease, and she feels that we're responsible. My greatest fear is that myself, or someone from my crew, has inadvertently spread a non native illness to that primitive society; but I don't want to jump to that conclusion until we've examined all of the facts._


	3. Chapter 3 - Diagnosis

**CHAPTER 3**

**DIAGNOSIS**

_Captain's Log, supplemental – We have established orbit around Equus Major 4. I have gathered the members of the original landing party in my quarters where we are to get in touch with Princess Celestia…_

"Rarity's being cared for at the Ponyville Hospital, if you remember where _that_ is…" Princess Celestia said.

"I'm sure Chief Engineer Scott can find the appropriate coordinates to beam down directly there…" Kirk said.

Celestia nodded. "I've already told Twilight Sparkle and her friends to expect you. Time is of the essence, Captain! Rarity may not hold out much longer!"

Kirk smiled reassuringly. "Don't worry, Princess! We'll get to the bottom of this…"

Celestia smiled back. "I have full confidence in you and your men's abilities! I'm expecting to hear some good news shortly…"

Then the image of Celestia faded from the mirror.

"Well, gentlemen!" Kirk began as he faced his men. "You heard the lady! Let's head down to Equestria…"

The doors to Captain Kirk's quarters swished open to let them all out into the hallway, and swished close behind them as they left the room.

"You know, I never really believed that that mirror actually _worked…"_ McCoy commented as they made their way to the Transporter Room.

"I told myself the _same thing_, until last night." Kirk said.

* * *

The forms of Captain Kirk, Mr. Spock, Dr. McCoy and Ensign Chekhov shimmered into existence in the hallway of the Ponyville Hospital underneath the warble of the transporter beam. They looked around and soon saw the familiar group of ponies standing in front of the bay window that undoubtedly looked into Rarity's hospital room. Twilight Sparkle was the first to notice them. She smiled and gasped as she trotted over to greet them.

"Captain Kirk!" she exclaimed happily. "You've _made _it!"

Kirk looked surprised. "Twilight Sparkle? Is that really _you!?" _

Twilight was confused. "Of _course _it's me! Who else could it be?"

"You've grown _wings!" _McCoy stated.

"Oh!" Twilight Sparkle said as she unconsciously extended them and looked back at them. "Well, to make a long story _short, _I undertook a very important test a short time ago imposed on me by Princess Celestia, and I passed with _flying colours; _so I guess you could say that… this was my _reward!" _She flashed a toothy smile.

"Fascinating!" Spock said as he raised his eyebrows.

Kirk finally realized that this was the unicorn Twilight Sparkle he had met previously once he saw her six point star cutie mark.

"Not only _that, _I've also recently been crowned a _Princess!" _Twilight Sparkle beamed.

"_Princess?" _Chekhov said in surprise.

"Mm hmm!" Twilight Sparkle showed pride.

"That's _extraordinary!" _Kirk commented.

"Can you _fly?" _McCoy asked.

"A little bit…" Twilight Sparkle said in answer. "I'm still getting used to them… but _Rainbow Dash _has been giving me flying lessons!"

As she said this, she put her left foreleg around the light blue coloured and rainbow mane and tail coloured Pegasus mare as she got beside her. "That's right! She's learning _quickly! _So you guys _finally _decided to show up, eh?" Rainbow Dash teased.

"Sorry to keep you _waiting!" _Kirk teased back.

Most of Twilight's friends had gathered around the humans once they saw that they had arrived.

"I'm so glad you're _here, _Dr. McCoy! I _missed _you…" Fluttershy smiled.

McCoy smiled back. "I missed you _too, _Fluttershy!"

They both shared a warm felt hug between them. Fluttershy hummed contently. "I'm even _more _glad that you're here, because _now _we can find out what kind of sickness Rarity has…"

McCoy smiled again. "That's what we're here for…"

Pinkie Pie didn't notice that the humans had finally arrived; but when she finally _did _notice, she gasped happily and immediately galloped in their direction. "CHEKHOV!" she exclaimed as she broke through the crowd of ponies and slammed right into the young Ensign. The impact knocked the wind right out of him, and before he knew it, he was on the floor being embraced by the impulsive pink mare.

"You'refinallyHEREI'msuperduperHAPPYtoSEEyouagaina ndImissedyouSOMUCH!" she babbled as she held him in her forehooves.

"N-nice you see you again TOO, Pinkie Pie!" Chekhov said as he cautiously returned the embrace. Pinkie Pie sighed contently.

"You always seem to attract the _weird _ones, don't you, Chekhov?" McCoy teased.

"It's a _gift!" _Chekhov smiled and shrugged.

Spike, who had been preoccupied with sadly watching Rarity lying in her hospital bed, right hand pressed against the bay window, never noticed the arrival of the humans until this point. He gasped when first caught sight of them. "They're finally _here!" _he exclaimed, then ran straight for Captain Kirk.

Kirk was surprised to see the diminutive dragon's face suddenly pressed up against his as he jumped up and grabbed him by his shirt collar.

"You gotta help her!" Spike said frantically. "She means A LOT to me, more than _anything! _PLEASE SAVE MY RARITY!"

Twilight Sparkle's magic hummed around him as she magically grabbed him and pulled him away from Kirk. "Get a grip, Spike!" she grumbled as she let go of him. He cried WHOA as he fell to the floor with a THUMP.

"Can Dr. McCoy really help her?" Twilight Sparkle asked Kirk.

"He's certainly gonna _try…" _Kirk smiled in response.

Nurse Redheart then stepped out of the hospital room, and pulled down her surgical mask. When she saw that Rarity's pony friends were gathered around the newly arrived humans, she immediately went over to them.

"Thank _goodness _you're finally here!" she said as she pushed through the crowd. "Which one of you is the Doctor?" she asked.

"I am!" McCoy said as he came forward. "What's going on?"

"Follow me!" Nurse Redheart said as she led Dr. McCoy to the bay window looking into Rarity's room. She gestured for McCoy to look inside. McCoy was surprised by what he saw.

"She looks bad off, Jim!" he told Kirk as he got beside him.

"Any idea what could be ailing her?" Kirk asked.

"Well, I can't say for sure until I examine her up close…" He then moved to enter the room.

"You can't go in there!" Nurse Redheart said as she stopped him just before the threshold. McCoy looked down at her questioningly. "Not without proper protection…" she smiled at him.

Minutes later, Dr. McCoy and Nurse Redheart walked out from a side room. McCoy was dressed in full surgical gear, complete with skull cap and surgical mask. Only thing was: The sleeves and pant legs were cut off at the midpoint, as it was not meant to be worn by humans! The black of his uniform pants could be seen; and since he wore his short sleeved dark blue Medical Officer's uniform short, you could still see his bare forearms.

"I know it's not exactly your size, Doctor" Nurse Redheart confessed "but it's the largest outfit we had. We normally keep it for rather large stallions…" She smiled embarrassingly.

"This'll do fine…" McCoy said.

"Looks good on you, Bones…" Kirk smiled and teased.

"Shut up!" McCoy grumbled as he pulled his surgical mask over his mouth, and followed Nurse Redheart into the hospital room.

As soon as he and the nurse entered the room, the two unicorn male Nurses enveloped them in a decontamination spell. That was their normal procedure for medical quarantines like this. McCoy took in the respirator and I.V. hooked up to Rarity, and glanced at the beeping electrocardiogram monitoring her heartbeat. _Primitive, yet effective, _McCoy thought to himself.

"Are you the human Doctor?" the male Earth pony Doctor asked as McCoy got beside the hospital bed.

McCoy nodded. "That's right. Dr. Leonard McCoy…"

"Doctor Heartthrob. Nice to meet you…" The Earth pony Doctor then extended his slipper covered hoof to McCoy. McCoy hesitated for a split second before he brought his fist up to meet the hoof in a simulated hoof bump. Though McCoy couldn't see his mouth underneath the surgical mask he was wearing, he was pretty sure the stallion was smiling.

He stood about four feet, 2 inches tall, quite large with a light gray coat and darker gray mane and tail. Though McCoy couldn't see his cutie mark underneath the surgical gown he was wearing, he figured it must be something medically related.

"How is she?" McCoy asked.

Heartthrob sighed. "Well, we've got her stabilized, but there's no telling how long she'll hold out. I've never seen anything _like it! _I've already tried every antibiotic we know. _No effect!"_

"Is she awake?" McCoy asked.

Heartthrob nodded. "I think so…"

"Rarity?" McCoy called. "Rarity, can you hear me!? It's Dr. McCoy! I'm here to _help _you!"

Rarity slowly raised her right eyelid and turned in McCoy's direction. After a few seconds, she turned her head away and closed her eye again.

"We think she knows where she's at" Heartthrob admitted. "but she doesn't seem to know who we _are…"_

McCoy raised an eyebrow and nodded. "That's helpful…"

He then brought out his medical tricorder. It warbled as he scanned Rarity with it.

"Interesting device!" Nurse Redheart commented.

"It's common among Starfleet Medical Officers…" McCoy smiled underneath his surgical mask.

While McCoy was examining Rarity, Kirk and his men took the opportunity to get caught up on recent events on Equestria with Twilight Sparkle and her friends.

Kirk learned that after being rescued from King Sombra's dungeon cave, the bat ponies Sombra had under his command were taken to The Crystal Empire's empirical city where they were kept in the Palace Dungeons to await trial. After King Sombra disappeared, they were unable to trace his whereabouts, and he remains at large.

The actual proceedings took place a short time after where the remaining sixty officers and soldiers of the original one hundred and fifty member bat pony garrison were tried at the same time in one gigantic trial that lasted for almost a week. During the rescue mission from the Crystal Empire Royal Guards led by Prince Shining Armour, most of the garrison had to be killed because they offered resistance. The rest were captured and taken prisoner.

In the end, all of the officers were convicted of high treason and sentenced to death by hanging from the gallows; while all of the simple soldiers were convicted of second degree treason and sentenced to twenty five years in prison. The executions were carried out a short time after, while the soldiers received their dishonourable discharge and were currently being kept in the Palace Dungeons while the new planned prison complex on the northern outskirts of the empirical city was being built. Twilight Sparkle told Kirk and his men that this new planned prison complex was necessary because the Palace Dungeons was already feeling the strain of overcrowding due to the many detainees that were being kept there.

The story of the trial reminded Kirk of The Nuremburg Trials of mid twentieth century Earth. World War 2 had just ended a few years prior; and while Germany was rebuilding its infrastructure, a whole bunch of Nazi war criminals were tried under a huge trial quite similar to the one the ponies had. Kirk heard that most of them suffered a similar fate as the bat ponies: Some were hanged while others faced lengthy prison sentences.

It was here that Kirk also realized that as utopian as the society on Equestria seemed to be, they were faced with the same social problems as on old Earth. Rampant crime forced the need to build elaborate prison complexes to house the criminals.

"Ah'll bet you boys saw some pretty interestin' things durin' ye're space explorin'?" Applejack asked.

"We have _indeed,_ Applejack…" Spock answered simply.

"But of _all _the worlds we've explored, your planet is certainly the most _interesting _of all…" Kirk said. "And nowhere else did we encounter such _wonderful _ponies…" Kirk smiled at Applejack.

"Aw, _shucks!" _Applejack blushed as she waved a dismissive hoof and turned her gaze away from the smiling Kirk.

Kirk then turned his attention to Spike. "And is it me, or have you _grown _a bit since last time we saw you?"

"Nope, you're not seeing things, I _have _grown a bit… We dragons tend to grow up _fast…" _he said proudly as he pretended to shine his claws while rubbing them against his chest.

Twilight Sparkle rolled her eyes at this.

"So, _Spock…" _Rainbow Dash began as she hovered to face the tall Vulcan. "When this is all over, how's about a little long distance race rematch, you and I? I'll even give you a _head start…"_ she bore her typical smug look on her facial features as she elbowed Spock in the chest.

Spock raised his eyebrows. "We shall see…"

Meanwhile, Pinkie Pie was babbling about all kinds of stuff at a hundred miles an hour to Chekhov, who faked interest. At one point, he rolled his eyes while Pinkie Pie wasn't looking at him.

Meanwhile, in the Quarantine Room, Dr. McCoy was just finishing up his scans on Rarity. He had reached a positive diagnosis, but he was quite perplexed by what he found.

"Well?" Doctor Heartthrob pressed.

"I know what disease she's come down with, but I'll need to talk to my Captain…" McCoy announced.

Heartthrob nodded. "Sure!" He then motioned for them to leave the room.

Both males made their way out of the room stopping momentarily to allow the two unicorn Nurses to decontaminate them. Nurse Redheart stayed behind to look after Rarity.

McCoy removed his surgical mask once he stepped out of the room, and immediately went to stand next to Kirk. "No doubt about it, Jim! She has _Vegan Chorial Meningitis…" _he announced.

Kirk was quite surprised at the news. "Are you _sure, _Bones!?"

"My tricorder doesn't lie! She has all of the symptoms…" McCoy admitted.

Kirk was dumbfounded. "But _how!? _How can that _be!? _We were decontaminated before we beamed down and when we beamed back UP…"

"I'll have to check the transporter logs. There may been some skips… or…" McCoy trailed off.

"Or _what?"_

"The only way she could've contracted the disease was through close physical contact… and you _were _in pretty close contact with her, if you recall…"

"Oh…" Kirk muttered as he looked embarrassed.

"I'll have to run further tests to confirm, but I'm pretty sure she caught the same bug _you _came down with six years ago, and it was a particularly virulent strain…"

"And I almost _died _from it!"

Doctor Heartthrob was growing more and more worried as this exchange was going on. His worry turned into _fear _when Kirk revealed that he almost died himself from the disease. Twilight Sparkle and her friends all bore looks of shock on their facial features at Kirk's revelation.

"But we've still got the vaccine aboard." Kirk then said. "You can administer it to her…"

"But it was configured for _humanoid _anatomies! A _pony's _anatomy is _far different!"_ McCoy exclaimed. "It may not even _work…"_

Kirk felt a growing mixture of anger and guilt. Anger that the vaccine they had on board the Enterprise might not work on Rarity, and guilt at bringing an alien disease on an alien planet, and afflicting one of its inhabitants. He reached out and grabbed McCoy by his shoulders.

"I don't care what it _takes, _Bones! _Help _her! Don't let her DIE! I don't want that kind of BLOOD on my hands!" He then stormed off.

He walked past a threesome of ponies who were making their way to the Quarantine Room. They glanced at him as he stormed past.

"Now _that _was a bit harsh…" Applejack commented with angry look in her eyes.

"We see that all the time…" Dr. Heartthrob admitted.

"Yeah… he has every right to feel _bitter…" _McCoy said.

The new trio of ponies arrived at the bay window. They were actually Rarity's parents and Sweetie Belle, Rarity's younger sister. The mare was a pink unicorn with violet coloured mane and tail. She had her mane tied in a beehive type of hairdo. The stallion was white with short brown mane, tail, and similarly coloured moustache. He wore a large straw hat that hid his unicorn's horn. Sweetie Belle hadn't changed all that much since the last time McCoy and his friends saw her. Only difference is: She looked to have grown a bit since then.

"We came as soon as we heard!" the mare said. "How is she?" she asked Dr. Heartthrob.

"We've got her stable, and we're working on a cure. Right, Dr. McCoy?"

"Yes… We're bound to have a cure soon…"

"So _you're _the human Doctor I've been hearing so much about…" the male unicorn said. "I'm Rarity's father. How do you do?" He extended his forehoof out towards McCoy.

"Pleasure…" McCoy said as he grasped it.

"And this is my wife and Rarity's mother… and you already know our younger daughter Sweetie Belle, I believe…"

"Yes! Hi, Sweetie Belle…"

"Hi, Doctor!" Sweetie Belle smiled.

Then they all approached the bay window to the Quarantine Room to see Rarity. Rarity's mother and Sweetie Belle both gasped simultaneously as they saw Rarity for the first time.

"Look at her!" Rarity's mother cried out to her husband. "I've never _seen _her like this… I'm _worried, _dear…"

"Don't worry, honey!" Rarity's father said as he placed a comforting hoof around his wife. "She's in _good hooves _here…"

"By _Celestia…" _Sweetie Belle cried out. "I've never _seen _Rarity so sick…" Her eyes became moist with sadness.

"Don't worry, Sweetie…" her mother said as she placed a comforting hoof around her. "Heartthrob and that human Doctor are working on a cure for her _right now…"_

Meanwhile, Heartthrob and Dr. McCoy were still discussing the finer points of Rarity's potential cure.

"Is it true what your Captain said…" Heartthrob began. "that you have the cure for the disease that's afflicting Rarity?"

McCoy nodded. "We do, but the vaccine is configured for the _human _immune system; however, I can configure it to be compatible with _ponies._ I have bio scans of some choice ponies on board the ship. I can use those to manufacture the antidote,but it's gonna take some _time…"_

"How long?" Heartthrob asked.

"Two or three hours…" McCoy answered.

Heartthrob nodded. "It should just be enough _time. _Is the disease _contagious?" _

"Not if it's properly _contained…"_

Heartthrob smiled. "Thanks for all your help!" He stuck out his forehoof to McCoy.

"No problem!" McCoy said as he grasped it.

"Doctor?" Nurse Redheart said as she poked her head out of the Quarantine Room. "You're needed…"

"Excuse me…" Heartthrob said as he put his surgical mask back on and reentered the Quarantine Room.

McCoy took out his communicator and opened it. "McCoy to Enterprise." He said into it.

"Enterprise, Lieutenant Ahura here…" came the voice of the Communications Officer.

"Put me through to Nurse Chapel in Sick Bay…" McCoy said.

* * *

Meanwhile, deep inside a cave in the frozen wastes at the foot of the Crystal Mountains, a sinister experiment was taking place. Inside a concealed room that was kept at a constant temperature of twenty-five degrees centigrade, rows upon rows of eggs were incubating. These were _changeling _eggs! They were brought here by the over two hundred or so changelings who defected from Queen Chrysalis' Realm in The Badlands and came all the way up North to hide from her and the vast Changeling Army they once belonged to.

They were lead by a rogue changeling named _Hugh_, who used to be Queen Chrysalis' right hoof male until he was promised freedom from The Collective and The Hive Mind he was once linked to. He has sacrificed much in the process, but the rewards of freedom and individuality were much greater than the price he had to pay. A hefty bounty was placed on him by Queen Chrysalis, and she would like nothing better than to have his head brought to her on a silver platter! The mere thought of this was enough to send shivers down his spine!

Hugh took it upon himself to care for the hundreds of changeling embryos that were brought here. The process to create a changeling was simple: The embryos were created using some changeling genetic material and a special cloning spell. Cloning spells were made illegal long ago in Equestria, but changelings had no compunctions against not using it to suit their own needs!

From there, the embryos are allowed to grow inside their own eggs; and once they hatched, they were moved into a Maturation Chamber where they undergo accelerated growth all the way up to adult form.

_Sometimes, _however, a changeling is created using a completely _different _method! It involves capturing a random pony and placing them inside a special cocoon where they undergo a slow assimilation process where their DNA is slowly altered into that of a changeling. This process was more time consuming, and the assimilation procedure was very delicate! One false move, and the pony would _die! _He has seen Queen Chrysalis do this on _numerous _occasions on ponies she had captured here and there! He was always told that the purpose of this process was "to add more distinctiveness to the changeling population".

Hugh, however, came to think of this process as most _distasteful! _He vehemently told his brethren _not _to engage in such activities to increase their numbers, after they defected! So far, they have obeyed his command.

Hugh was so busy looking after the precious embryos that he failed to notice the pony who entered the chamber behind him. "Report!" the pony said in a deep male voice.

Hugh was started by the voice, and immediately turned to see who it was. He breathed a huge sigh of relief when he saw who it was. "_Sombra! _You _startled _me! I didn't hear you come in…" Hugh smiled nervously.

Sombra smiled and humpfed.

King Sombra was the main reason why Hugh and his changeling minions defected in the first place. He had promised them freedom from enslavement in The Badlands and from Queen Chrysalis' tyranny. He had also promised them places of honour in the New Order once he took over Equestria once more! It was under these promises that Hugh adopted Sombra as his new _Master, _and his changeling minions became a part of King Sombra's new Army.

"How are your _babies _doing?" Sombra asked.

"_Splendidly, _Master!" Hugh said. "Soon they will hatch and move on to maturation…"

"_Excellent!" _Sombra smiled. "My plan is almost coming to fruition! Soon I will have a changeling Army strong enough to defeat the combined Crystal Pony Armies. Then I will _dethrone _The Crystal Princess and her loverboy _Prince _andassume my rightful Sovereignty of The Crystal Empire _once more!_ From there, taking over Equestria will be _easy as pie…" _he grinned wickedly. "… and I have _you _to thank for it all…"

"Thank you, Master!" Hugh said as he smiled and bowed.

"Everything is proceeding _exactly_ as I have foreseen!"King Sombra said.

Then he started to laugh evilly. His wicked laughter increased just as a nearby egg began to crack open as the changeling hatchling inside struggled to get out. Hugh immediately moved to assist the squealing hatchling in getting free from its shell and preparing it for the Maturation Chamber. Sombra continued to laugh evilly at the sheer genius of his plan for conquest.


	4. Chapter 4 - Vaccination

**CHAPTER 4**

**VACCINATION**

_Captain's Log, Star Date 5192.9 – Just three hours after Dr. Leonard McCoy diagnosed Rarity with Vegan Chorial Meningitis, he has synthesized a prototype for a vaccine that would be compatible with the alien pony's anatomy. He had just beamed to the planet's surface to administer it to her. We have high hopes that it will counteract the virus that's currently afflicting her._

The HISS of the hypodermic injector could be heard as Dr. McCoy inserted the antidote into Rarity's blood stream via her right foreleg. He then brought out his medical tricorder and began to take readings. It's warbling sound could be heard as he scanned all up and down Rarity's body.

Dr. Heartthrob and Nurse Redheart looked on in anticipation of some good news. "Well?" Dr. Heartthrob prompted.

"It's _working!" _Dr. McCoy said happily. "The vaccine's taking effect!" You could not see his smiling lips, because it was hidden underneath his surgical mask, but his eyes betrayed his joy.

"Well, _that's _a relief!" Dr. Heartthrob said as he breathed a heavy sigh.

"What happens _now, _Doctor?" Nurse Redheart asked.

"She should start feeling better within the hour…" McCoy answered. "I'd like you to keep her under observation for another twenty four hours, though; in case there are any… _complications…"_

"Will do, Doctor!" Dr. Heartthrob said smiling under his own surgical mask.

Then he noticed Captain Kirk watching intently from the hallway outside of the room. "I'd better go give the good news to my Captain…" McCoy announced.

"Right behind you!" Dr. Heartthrob said as he followed McCoy outside.

After being decontaminated by the two male unicorn Nurses, Dr. McCoy and Dr. Heartthrob both stepped out of the room to join Captain Kirk and Mr. Spock, who was standing beside him.

"Great news, Jim!" Dr. McCoy said as he pulled down his surgical mask. "The prototype for the vaccine actually _works! _Rarity will be her old smiling self full of vanity _in no time…"_

Twilight Sparkle and her friends all jumped up and cheered at the news they overheard.

Kirk smiled in relief. "That _is _great news! Well done, Bones!" He patted Dr. McCoy on his left arm in congratulations.

"But we're not out of the woods yet…" McCoy then admitted. "We'll need to inoculate the entire pony population of this planet to prevent the disease from spreading…"

Kirk's facial expression then turned more serious. "Oh! I forgot about that…"

"But _Doctor…" _Dr Heartthrob began. "Do you realize how many _millions _of ponies there are in Equestria!?"

"Four million seven hundred and seventy-five thousand eight hundred and ninety one…" Spock answered.

Everybody looked at him curiously.

"…Based on last sensor readings…" Spock said simply.

"Well, we'll just have to manufacture enough vaccinations for every last one of them…" McCoy said, breaking the sudden awkward silence. "And with that many ponies on this planet, that means my Medical Staff will have to work around the clock to get everything done quickly…"

"But… what about the _other _species on Equestria?" Twilight Sparkle asked. "The Griffons… the Minotaurs…"

"We'll just have to manufacture antidotes for them, too." Dr. McCoy said. "Now that we know the procedure for making it, we can synthesize vaccines compatible for _their _anatomies, and give it to their own Doctors to administer it amongst their populations…"

"In the meantime, I'll have to contact Starfleet to gain approval for this… impromptu mission…I have a feeling that with _that _many ponies to inoculate, we're gonna _be _here for awhile." Kirk said.

"The better part of two weeks, I would say…" Spock said simply.

"Thank you, Mr. Spock!" Kirk said with some irritation as he brought out his communicator to signal the Enterprise.

Meanwhile, Sweetie Belle turned away from the bay window to face her mother. "Now that Rarity's gonna bet better, can I go join Apple Bloom and Scootaloo at our club house?"

Her mother smiled down at her. "Of course, Sweetie…"

The little filly beamed. "Thanks, mom!" she said as she galloped off.

"Just be home in time for dinner!" her mother called out to her.

"I will!" Sweetie belle called back.

"Well, Twilight Sparkle…" Kirk began. "Or should I call you _Your Highness _now?"

Twilight Sparkle giggled. "I'm still not used to the _Your Highness _part, so you can still call me _Twilight."_

"Well, ya _better _get used to it. Lotsa ponies'll be callin' ya _that _from now on!" Applejack said with a smile.

Kirk smiled himself. "All right… _Twilight… _I was gonna say that while Dr. McCoy and I beam back up to the ship, Mr. Spock's gonna stay on the surface to keep an eye on Rarity, in case she… _relapses…"_

"I doubt it, though…" McCoy said in reassurance. "The vaccine I designed is _foolproof…"_

"In the meantime, you can report what went on here to Princess Celestia…" Kirk told Twilight.

"Will do! Spike?"

"_Yes, _Twilight…" Spike said as he finally tore himself away from the bay window looking into Rarity's room.

"But what about Chekhov?" Rainbow Dash mentioned.

Everyone turned to see Pinkie Pie bouncing around Chekhov and babbling on at a hundred miles an hour about everything that's happened in Ponyville since the Enterprise last left while Chekhov just stood there feigning interest. His eyes betrayed the look of boredom and annoyance.

Kirk chuckled. "Looks like Pinkie Pie's gonna keep him busy for awhile. He'd might as well stay…"

"Poor him! Ah certainly understand how he feels…" Applejack said.

"Yeah… She gets that way around everypo… every_body… _she really likes…" Rainbow Dash said.

Kirk and Dr. McCoy then moved away from the group. Kirk opened his communicator again. "Enterprise, two to beam up!"

Soon after he closed his communicator, the humming sound of the transporter beam could be heard as the forms of Kirk and McCoy disappeared in a cloud of sparkles.

* * *

Later that day, in a rickety looking tree house on the far southern edge of Sweet Apple Acres, the fillies Applebloom, Sweetie Belle and Scootaloo were having a meeting.

These were the Cutie Mark Crusaders! They were three friends who have made it their own personal mission to discover their own special talent and finally earn their own personal cutie mark. They have tried many times at many different things, and always ended up _failing _miserably; but they were still as determined as ever to earn their much desired cutie marks.

"So what kinda cutie mark crusadin' are we gonna do _today, _girls?" Applebloom asked.

Sweetie Belle sighed. "I don't know! I'm fresh out of ideas…"

Scootaloo spoke up. "Well… we could try going _space exploring _again… I've kept the ship we've built… _mostly…"_

"OOOOOOOOOH NO!" Sweetie Belle said immediately. "I'm not trying _that _again! We almost got _incinerated _the last time…"

"In sinnerWHAT!?" Applebloom asked in confusion.

Sweetie Belle blinked. "We almost got burned to a _crisp!"_

"Oh, YEEEEAHHH! NOW ah remember!" Applebloom said. "If it weren't fer ma big sister an' _Rarity _bein' there, we'd've been _toast _fer SURE!" She then glared angrily at Scootaloo.

"HEY! I said I was _sorry…" _Scootaloo said right away. "Besides, it was _Sweetie Belle's _idea to use that _firestarter _spell to get the ship going…"

Applebloom glared angrily at the young unicorn filly, who grinned nervously as she shrugged.

"But I was _thinking_… maybe we could do something _different _this time…" Scootaloo said.

"Lahk _what!?" _Applebloom asked.

"Maybe we could ask _Spike _to help…"

"_Spike!? _What does _he _know about space explorin'!?"

"He's a _dragon! _He must know _something… _OR… we could ask Captain Kirk, now that _he's _back..."

Applebloom shook her head. "That won't work, Scootaloo! He's got that _Prime Directin' _thing goin' for him, or _whatever _it's called…"

"Meaning?"

"_Meaning _that he's not allowed to tell us what he knows about space explorin', or how he builds that fancy _spaceship _o' his…"Applebloom said as she pointed in the direction of the sky where the Enterprise was in orbit.

"Oh…" Scootaloo said in realization.

Then they noticed that Sweetie Belle had remained unusually quiet this whole time. They both turned to face her.

"Sweetie Belle, ya haven't…" Applebloom's phrase was cut short when she noticed that something was not right with her friend. "Are ya all right!?" she asked in a concerned voice.

"What's wrong?" Scootaloo asked equally concerned.

She looked to be quite woozy as had her right forehoof to the side of her head. "I… I don't know… I just feel _dizzy _all of a sudden…"

"Maybe you should go lie down…" Scootaloo suggested.

"Yeah, I…" Sweetie Belle began, but cut short her phrase as her eyes rolled to the back of her head and she collapsed to the floor.

"SWEETIE BELLE!" Applebloom cried out as she ran to the aid of her friend. She lifted her head up and noticed that she was unconscious. "We gotta get 'er to the _hospital,_ RIGHT NOW!" she told Scootaloo.

"Agreed…" Scootaloo said as she helped Applebloom carry the unconscious Sweetie Belle straight to the Ponyville Hospital.


	5. Chapter 5 - Epidemic

**CHAPTER 5**

**EPIDEMIC**

_Captain's Log, Star Date 5193.2 – After three hours of intense negotiations with Starfleet Command, I've finally gained approval for the mission to inoculate Equestria's population from Vegan Chorial Meningitis. Dr. McCoy and his medical staff are hard at work producing the vaccine we need as we speak._

The turbo lift doors leading to the Enterprise's Bridge swished open to reveal Dr. McCoy. He immediately went to stand next to Captain Kirk, who was rooted in his Captain's chair.

"The first batch of vaccine is ready for distribution. Just thought you should know…" he said.

"Very good, Bones!" Kirk said in reply.

"I hear the negotiations with Starfleet to gain approval for this mission were pretty _intense…"_

Kirk smiled. "You're _right, _Bones. It took a fair bit of convincing to get Admiral Nagura to put her seal of approval on this mission… in exchange for a _huge favour…"_

McCoy raised an eyebrow. "Well, I'll leave that between you and _her…"_

"Captain, message coming in from Mr. Spock…" Ahura announced from her Communications posting.

Kirk pressed the intercom button located on his armchair. "Kirk here."

"Captain…" Spock's voice said through the intercom. "Another patient exhibiting the symptoms of the disease has arrived at Ponyville Hospital. It is Rarity's younger sister. _Sweetie Belle, _I believe her name is…"

"Tell Spock I'll be right down!" McCoy said as he rushed to the turbo lift.

"Spock, Dr. McCoy's on his way down with the vaccine…" Kirk said.

"Acknowledged. Spock out." Spock said.

Kirk then pressed the intercom button again to close the communicator channel.

* * *

Roughly fifteen minutes later, Dr. McCoy was in Sweetie Belle's room at the Ponyville Hospital. His hypodermic injector HISSed as he injected the vaccine into the young filly's blood through her right forelimb. Like her big sister just a few hours before, she was hooked up to a respirator and heart monitor, as she was totally unconscious.

Dr. McCoy then took out his medical tricorder. It warbled as he scanned Sweetie Belle's vitals. He didn't bother putting on one of the hospital's surgical gowns or face masks, since he now knew what disease Sweetie Belle was afflicted with. Doctor Heartthrob and Nurse Redheart didn't wear surgical gowns either, as they were now inoculated from the disease.

Dr. McCoy's facial expression quickly turned to worry. "Something's _wrong!"_

Dr. Heartthrob and Nurse Redheart shared his worry. "What is it, Doctor?"

"She's not reacting to the vaccine, not like Rarity did…" he said.

Both ponies immediately pulled up the surgical masks they happened to have over their mouths.

"I'll double check…" McCoy said as he scanned Sweetie Belle's vitals again.

A soft moaning sound from behind them made Dr. Heartthrob and Nurse Redheart turn. "AH! Rarity… You're finally awake!" Dr. Heartthrob said happily.

Rarity rubbed the sleepiness out of her eyes as she focused on the pony Doctor and Nurse Redheart. "What _happened?" _she asked groggily.

"You came down with a severe disease." Dr. Heartthrob said. "It was touch and go there for awhile, but you're out of it _now, _thanks to Dr. McCoy…" He gestured towards the human Doctor, who was still scanning Sweetie Belle.

"Doctor McCoy!?" Rarity asked in surprise. The Starfleet Medical Officer just briefly glanced at her as he continued with his scans. She gasped when she saw who was in the hospital bed next to her. "SWEETIE BELLE!" she exclaimed.

"It's okay, Rarity!" Dr. Heartthrob said reassuringly. "Your little sister came down with the same disease _you _did, but Dr. McCoy's working on making her _better. _Right, Doctor?"

Before Dr. McCoy could answer, his communicator BEEPed. "McCoy here…" he said into it as he opened it up.

"This is Mr. Spock…" McCoy looked up to see the Vulcan looking at him through the bay window from the hallway. "Is everything all right?"

"No, everything is NOT all right, you green blooded, POINTY EARED…" he shouted into his communicator.

Spock simply raised his right eyebrow at this.

"Sorry…" he said in a much softer tone.

"There is no need for emotionalism, Doctor." Spock said. "Please make your report…"

"Sweetie Belle's not reacting to the vaccine like Rarity did…" McCoy admitted.

Spock raised his eyebrow again. "Curious…" he said. "Any idea as to _why?"_

Dr. McCoy became pensive. "I may have an idea, but I need to be _absolutely sure. _I can't do much down here, though. I'll need to beam myself and Sweetie Belle up to Sick Bay…"

"Doctor, I _must _point out that-"

"Don't lecture me on the PRIME DIRECTIVE that we already KNOW!" McCoy said forcefully. "In THIS case, however, my HYPOCRATIC OATH takes precedence!"

Spock raised his eyebrow a third time. "Knowing full well your determined stubbornness in these situations, I have no alternative but to let you _proceed…"_

"THANK you!" McCoy said before opening up a channel to the Enterprise. "McCoy to Enterprise, put me through to Scotty in the Transporter Room."

"All right, Doctor." Ahura said.

"Scott here, Doctor." Came the voice of the Chief Engineer through the communicator seconds later.

"_Scotty, _two to beam directly to Sick Bay! Medical emergency!"

"Acknowledged…" Scotty said.

McCoy noticed the concerned look of the ponies as he closed his communicator. "Don't worry! She's in good hands…" he said with a reassuring smile.

Just then, the hum of the transporter beam could be heard as the forms of Dr. McCoy and Sweetie Belle disappeared in that familiar shimmer of light.

"D-did Dr. McCoy just beam Sweetie Belle…" Rarity said after a few moments of silence, pointing towards the sky.

"I think so…" Dr. Heartthrob said with a nod.

"Will she be _all right?"_ asked a concerned Rarity. Even though she thought her little sister to be an annoyance sometimes, deep down inside, she loved her a great deal.

Dr. Heartthrob sighed. "I _hope _so…" he said before walking out of the room.

After watching Dr. Heartthrob leave, a smiling Nurse Redheart turned to face Rarity. "Well, you must be _hungry. _After all, you've been out for almost twenty-four hours."

Rarity smiled back. _"Yes,_ a proper meal would be in order."

Still smiling, Nurse Redheart left the room to go prepare the meal of hospital food, leaving Rarity to contemplate the fate of her younger sister.

* * *

_Captain's Log, Supplemental – We've encountered a setback in our mission: Sweetie Belle, Rarity's younger sister, wasn't immunized by the vaccine we've prepared. Dr. McCoy has beamed the young filly to Sick Bay to run further tests._

"I'll need to run a biopsy to confirm, but it looks like the virus may have already _mutated _into a whole new strain…" McCoy told Captain Kirk.

In the background, Sweetie Belle was lying on one of the Sick Bay's bio beds, completely unconscious. She was fitted with a girl's sized Sick Bay gown, and was being looked after by Nurse Christine Chapel. The rhythmic THUMPing of the vitals screen behind the bio bed told everyone that Sweetie Belle's heart was still beating at a steady pace.

Kirk's facial features betrayed concern as he pondered what McCoy just told him. "So what happens _now?"_

"Well, we'll have to recall whatever vaccines that were already distributed down there and _start from scratch…"_

Kirk nodded. "And your decision to beam Sweetie Belle directly to Sick Bay was, of course, the _right _one…" Kirk then glanced towards the unconscious Sweetie Belle. "How is she?"

"Well, I've got her stabilized, but we're gonna need to come up with a vaccine to cure her _soon! _I've already got my medical staff working on it…"

The Sick Bay's intercom whistled to indicate an incoming message. Kirk moved to the speaker on the wall and pressed the button to open the channel. "Kirk here."

"This is Mr. Spock…" came the voice of the Vulcan Science Officer. "I have here two fillies who wish to beam aboard the Enterprise. They claim to be close friends with the filly in your Sick Bay, and they are _quite insistent…"_

Kirk and McCoy each shared a look, but it was up to Kirk whether or not to allow these two fillies to beam aboard. "All right, Mr. Spock. Have Scotty beam those two fillies directly to Sick Bay…"

"Aye, Captain. Spock out."

Kirk then closed the intercom.

Moments later, the warbling sound of the transporter beam could be heard as the forms of Scootaloo and Apple Bloom materialized into the Sick Bay. They both gazed at their new surroundings.

Apple Bloom gasped as she spotted the unconscious Sweetie Belle lying on the bio bed. "Sweetie Belle!" she exclaimed as she rushed to her friend's bedside. Scootaloo followed behind. They were both stopped by Nurse Chapel just a few feet away from the bio bed.

"Hey! HEY! Take it _easy!" _Kirk said as he came to stand in front of the two fillies. "Your friend's being _well looked after, _don't you worry…" he said reassuringly.

While Applebloom's facial features expressed great concern for her friend, Scootaloo couldn't help but gaze at the Sick Bay she was in. "WOW! This is a nice looking SHIP you've got here, Mr. Kirk!"

Kirk smiled. "I thank you! It's a lot bigger than _this, _of course; AND it serves us _well…"_

"I don't doubt _that!" _Scootaloo said. "I'd like to learn more about-"

Scootaloo cut her phrase short as she suddenly felt dizzy. She had just enough time to raise her right forehoof to the side of her head before she collapsed from unconsciousness. Nurse Chapel quickly caught her just before she hit the floor. "Doctor!" she exclaimed.

"Put her in a bio bed, STAT!" McCoy ordered.

Nurse Chapel carried the young Pegasus filly away in order to get her ready for a bio bed.

"You too, Apple Bloom." McCoy announced.

The young Earth pony filly looked at McCoy questioningly. "But ah feel _fine!" _Apple Bloom complained.

"_Still, _I'd like to keep you here under observation. You've been exposed to the virus as well, and it's only a matter of time before _you _get sick as well…"

Apple Bloom sighed reluctantly. "All _right! _Ye're the _Doc, _Doc!"

Apple Bloom then went to get herself outfitted with a bio bed gown by Nurse Chapel.

The Sick Bay's intercom whistled again to indicate another incoming communication. "Kirk here." The Captain said as he opened the channel.

"This is Mr. Spock again, Captain." Came the voice of the Vulcan. "Several other pony patients have just arrived at the hospital all exhibiting symptoms of the disease…"

Kirk and McCoy shared a look of great concern as they were both shocked at this revelation.

"All right, Mr. Spock! Have the medical staff down there issue a quarantine…" Kirk ordered.

"Already being looked after, Captain." Spock announced.

"God bless those ponies…" Kirk said under his breath. "Very good, Mr. Spock! Do what you can to help down there, and stand by for further instructions…"

"Acknowledged. Spock out."

Kirk closed the intercom channel again.

"It's _exactly _as I feared, Jim!" McCoy admitted. "Not only has the disease mutated into a whole new more virulent strain, it's become _airborne!"_

Kirk grew even more concerned as he let what McCoy just told him sink in. "Do what you _can, _Bones, for the sake of this planet's civilization! And keep me upraised of your findings…"

Kirk didn't wait for an answer as he left. The Sick Bay doors swished open to allow him to exit out into the hall.

The sound of Apple Bloom's sobbing from behind made Dr. McCoy turn around. Nurse Chapel did her best to comfort her as she helped her into a bio bed, but it did nothing to ease the young filly's sadness.

"I've got a lot of work to do…" Dr. McCoy told himself as he made his way to the lab to help in finding a cure for the disease that was now starting to infect the entire pony population of Equestria.

* * *

Meanwhile, in a hidden cave near the North Pole, King Sombra was sitting in his makeshift stone throne waiting for his trusted right hoof, the changeling called Hugh, to come deliver his report. He had given him specific orders a half hour ago, and was already growing impatient at hearing back from his minion.

Finally, Hugh appeared in the "throne room" to stand a few feet away from Sombra and bowed deeply before him. Sombra returned the bow as he waited in anticipation for Hugh's word.

"All is _ready, _Master!" Hugh announced. "Just as you've ordered!"

"Excellent!" Sombra said with a wicked grin as he got up from his "throne". "You have done _well, _my minion! You shall be _greatly rewarded, _once this is all over…" he said as he cantered passed Hugh.

"Thank you, Master!" said a smiling Hugh as he fell in step behind Sombra as they left the "throne room"

They headed down a dark passageway that leads to a rocky ledge that acted as a balcony. As soon as Sombra and Hugh appeared on the "balcony", they were met by a large ruckus of cheering and roaring; for below them stood a grand army of changelings, twenty thousand strong! They all wore dark grey armour that matched King Sombra's coat colour with his dark crystal symbol emblazoned on their chest plates. They also carried long spears!

Some changelings at the forefront carried large tall banners with the same dark crystal symbol at the bottom, and a drawing of his menacing roaring face, complete with his bright green eyes with red pupils and purple smoke emanating from them, at the top.

Sombra let his fanged teeth show in an evil grin as he let the cheers and roars of his loyal army continue for several more minutes. Hugh shared Sombra's evil grin as he smiled wickedly in satisfaction at the Changeling Army that he has helped create with the two hundred changelings who defected with him from Queen Chrysalis' Empire in the Badlands.

Once King Sombra's decided that he's had enough, he raised his left forehoof in the air as a signal for complete silence. It didn't take long for the din of the Changeling Army to die down. He then began his speech.

"My friends and loyal members of my Changeling Army, today's the day that we embark on our quest towards our _destiny! _

"For too long, the pony races of Equestria have lived under Celestia's _tyranny! _The time has come to restore the New World Order of EONS PAST!"

The changelings erupted into cheers and roars again as they waved their long spears in the air. Sombra grinned wickedly as he allowed this to continue for several minutes. He then raised his hoof again to call for silence. The din immediately died down.

"TODAY, we take the first steps of our _glorious conquest _by taking back The Crystal Empire from The Crystal Princess and her "Prince Charming", then we will use the magical powers of their crystals and the famous Crystal Heart to conquer ALL of Equestria!"

The changelings cheered and roared again. This time, however, King Sombra raised his forehoof immediately to call for silence. The changelings immediately complied.

"We are _destined _for this greatness, for long ago…" Sombra became pensive. "Long ago… I was a _Prince _with POWER over _millions! _Then I named myself _King _as I established my New World Order where everypony lived in _prosperity!"_

The changelings cheered and roared again. Sombra didn't raise his forehoof this time. Instead, he shouted loud enough to be overheard over the din.

"ONWARDS towards our DESTINY! Today, The Crystal Empire; tomorrow, THE WORLD!"

He stood on his hind legs and raised his forehooves in the air as he said this last phrase.

The changelings cheered and raised their long spears in the air one last time, then started marching towards The Crystal Empire where they were to begin their attempt at conquering Equestria.


	6. Chapter 6 - Siege

**CHAPTER 6**

**SIEGE**

_Captain's Log, Star Date 5193.4 – Barely one hour ago, we've received news that the disease has mutated into a fast acting, more virulent strain that's become airborne; and it was spreading quickly. Dr. McCoy is currently looking after three of the inhabitants from the planet below in our Sick Bay. He has just called me down to give a report describing an idea he had on how he can find a cure for the disease, which was spreading like wildfire. _

In Sick Bay, the unconscious forms of Sweetie Belle and Scootaloo were lying in their own respective bio beds, while Apple Bloom was wide awake in her own bio bed to the left of Scootaloo. They were all wearing their own light blue girls' sized Sick Bay gowns that turned out to be just their size. Apple Bloom looked to be very sad and worried. Nurse Chapel has hardly left her side while Dr. McCoy continued to monitor the vitals on all three.

The vitals monitors on the wall behind the bio beds continued to measure the fillies' heart rates, and made the tell tale THUMPing sound that told Dr. McCoy and Nurse Chapel that their hearts were beating steadily. They weren't perfectly synchronized, though; so they made a THUMP THUTHUMP THUMP THUTHUMP sound. Eventually, one would overtake the other; and they would sound in sync for a second or two, but then immediately go back into the erratic pattern of THUMPs again.

The Sick Bay doors SWISHed open to reveal Captain Kirk as he rushed into the room. "You said you had an idea as to how you can manufacture a cure, Bones?" he immediately asked the Doctor.

"Yes!" Dr. McCoy answered. "I feel the key to finding a cure hinges on young _Apple Bloom _here. She's not exhibiting any symptoms of the disease, though she's been _heavily exposed_ to it; which tells me that she may already be _immune_. I feel that if we can manufacture a serum from her blood, we can _quickly _develop a new vaccine to cure _all _of them."

Kirk nodded. "That gives us something to go on… But… can you develop a vaccine compatible to _all _of them so _quickly!?"_

McCoy smiled. "I think so. Even though they have eleven different blood types, our technology is _advanced _enough to make a _universal _vaccine in such a short period of time that it won't cause any _conflicts…"_

Kirk nodded again. "All right, Bones. Proceed…"

McCoy moved over to the work table next to Apple Bloom's bio bed where he prepared a hypo to draw the young filly's blood with.

"Whatcha doin' _now, _Doc?" Apple Bloom asked.

McCoy smiled at the little filly. "I'm preparing to draw a sample of your blood…"

"Why?"

"It's to help me figure out why you haven't gotten sick from the disease while your friends over there _did…_ Hopefully, it'll help me find the _cure…"_

"Oh…" Apple Bloom shrugged. "Must be that Apple family _resilience _mah big sister keeps talkin' about…"

"Well, I'd like to be the judge of _that…" _McCoy said as he brought the hypo drawer up to Apple Bloom's left foreleg.

"Uhh…" Apple Bloom retreated. "Not that ah'm… _afraid, _or nothin', but… will it _hurt _much?"

McCoy smiled reassuringly. "I guarantee you won't feel a _thing…"_

Feeling reassured, Apple Bloom relaxed.

Dr. McCoy pressed the hypo up against Apple Bloom foreleg. It HISSed as it drew some of the young filly's blood into the small plastic tube that was attached to it.

"Get this down to the lab _right away!" _Dr. McCoy ordered as he handed the hypo to Nurse Chapel.

"Yes, Doctor." Nurse Chapel said as she took the hypo and left.

He smiled again at Apple Bloom. "You're a brave little filly, Apple Bloom! You may not realize it _now, _but you're helping us out a _great deal!"_

Apple Bloom smiled up at Dr. McCoy. "Ah'm _glad!" _

Dr. McCoy turned to leave.

"Doc?" Apple Bloom said, which made McCoy turn back to face the young filly.

"Can ya… _really _help mah friends?" she asked with a worried look on her facial features.

Dr. McCoy smiled and laid a comforting hand on Apple Bloom's left shoulder. "I promise you I'm gonna do _everything in my power_ to saveyour friends…"

"He's _right, _you know!" Captain Kirk, who had been observing the situation, said with a smile. "McCoy's the _finest _Medical Officer in Starfleet. If he says he can cure your friends, you can bet your money on _that…"_

Apple Bloom smiled at Kirk. "Thank you."

"You're welcome." Kirk replied.

"Ah sure _wish _there was somethin' ah could _do, _though! It sure is _borin' _just lyin' here in this _bed _starin' at the _walls _all the time…"

Kirk pondered. "I see no reason why you can't sample some of our literature from the ship's Library. Something simple, Bones; like children's books?"

Without saying a word, Dr. McCoy pulled a nearby bio bed console up to Apple Bloom's lap.

"Yeah… Twalaght Sparkle's always sayin' how _important _it is ta read _books… _Might as well get _started…" _Apple Bloom smiled.

The Sick Bay's intercom whistled. Kirk left McCoy to get Apple Bloom set up to go answer it.

"Kirk here." The Captain said after he pressed the button to open the channel.

"Spock here, Captain." Came the voice of the Vulcan. "Princess Celestia requests urgent communication with you via the magic mirror that is in your quarters…"

"Acknowledged! Kirk out." Kirk then closed the intercom's channel.

Without saying a word, he left the Sick Bay on his way to his quarters. The Sick Bay doors SWISHed open to allow him out into the hall, and then SWISHed closed behind him once he left.

* * *

Minutes later, Captain Kirk entered his quarters and immediately went to stand in front of the magic mirror where the image of the ruler of all Equestria was patiently waiting. "AH! There you are, Captain Kirk! Thank you for meeting with me on such short notice…"

Captain Kirk bowed. "My pleasure, Your Highness…"

"I've just received word from Princess Mi Amore Cadenza of The Crystal Empire. It seems they are facing an imminent _crisis _up there right now…"

Kirk grew worried. "What sort of _crisis?"_

"I'd rather let my niece herself explain this to you…" Princess Celestia then closed her eyes and called forth an alicorn spell. The hum of her alicorn magic could be heard as her magical aura surrounded her alicorn's horn. The image of Celestia moved to the top of the mirror while another panel appeared underneath. "Princess Cadence…" Celestia called. "Princess Cadence, are you there?"

The image of the Crystal Princess then appeared in the panel at the bottom. "Yes, Auntie! I am here! Greetings, Captain." She told Captain Kirk.

Kirk bowed again. "Your Highness…"

Kirk was amazed that Princess Celestia called forth what could best be described as a "magical conference call" through this mirror that he had. This told him that their alicorn magic must be _very _powerful!

"Your aunt tells me that there's a _crisis _of some sort in your Empire?"

Princess Cadence nodded. "Yes! The disease that you accidentally brought here has reached The Crystal Empire. Many of my loyal subjects have taken ill over the past twenty-four hours. Our hospitals are being _overrun, _and there's general panic amongst the crystal pony population."

"Dr. McCoy is working on a cure for the disease _as we speak…" _Kirk said reassuringly.

"I don't doubt the abilities of your Doctor, Captain; but there's _more…"_

Kirk grew worried again. "_More, _you say!?"

Cadence nodded. "Yes. But I'd rather let my husband give you the details…" She then gazed to her left.

"Hello, Captain!" Shining Armour said as he came into view. He was wearing his suit of armour identifying him as the Captain of The Royal Guard. He was holding his helmet in his right foreleg.

"Your Excellency…" Kirk said as he bowed again.

"Actually, you can just call me _Shining… _or _Captain, _like yourself, if you prefer…"

Kirk smiled. "All right… _Shining… _your wife tells me that there was something _more _to this crisis than the disease?"

Shining Armour nodded. "Yes. A vast Changeling Army is amassing outside the northern part of the Imperial City. My scouts report that there's at least _twenty thousand _of them…"

Kirk's eyes betrayed his emotion of shock.

"They're being led by King Sombra, and they've already asked for our _unconditional surrender…" _Princess Cadence said.

"They've given us a _two hour ultimatum…" _Shining Armour said.

"But… you have _troops _at your disposal to defend your city, should they attack?"

Shining Armour nodded. "Yes. An entire garrison was transferred here from Canterlot shortly after we got married. _Plus, _we have a lot of recruits from the crystal pony population. But _a lot _of them have already taken ill from the disease, and are in _no condition to fight…"_

Kirk stayed silent for a few moments as he took this in. "How many of your troops are _actually _fit for duty?"

Shining Armour sighed as he looked to the floor. "Less than _three thousand…"_

Kirk was in shock again at this revelation.

"With many more, I fear, being _unfit _for duty by day's end…" Shining Armour continued.

It was Kirk's turn to look to the floor.

"I know that your Prime Directive prevents you from interfering in the affairs of other worlds," Princess Celestia began. "but I _also _know that you have _technology _and _weapons _far beyond even our _current _capabilities. If King Sombra is allowed to take over The Crystal Empire, he will only bring about a dreadful reign of _tyranny _and _despair _that will eventually stretch throughout _all of Equestria!_

"That is why I say that _any assistance _you can give us to thwart his plans will result in _our eternal gratitude _to you and your _people…"_

Kirk remained silent as he continued to gaze at the floor of his quarters, pondering that to do next. "Remember the Alamo…" he muttered under his breath.

"What's _that _supposed to mean!?" Shining Armour said suddenly.

Kirk looked up, genuinely confused. "What!?"

"What you just _said… _Remember the…" Shining Armour prompted.

"Oh…" Kirk said, forgetting that the ponies had a keen sense of hearing. "It's in reference to an old legend among my people about a famous battle that took place long ago where a small group of soldiers faced _insurmountable odds. _I mean, they were _literally _outnumbered a _hundred _to one, but STILL managed to defeat their enemy…"

Shining Armour smiled. "Sounds kind of like what _we're _facing right now, isn't it?"

Kirk smiled and nodded. "I can tell you more about it _later, _if you'd like…"

"I'd _like _that!" Shining Armour said.

"I'll see what I can do. I'll contact you later…" Kirk said.

"Hopefully not _too much _later." Princess Celestia said. "Time is of the essence…"

"And thank you for considering our plea…" Princess Cadence said.

The two alicorns and one unicorn then bowed to Kirk as their images faded from the magic mirror, which then went black.

Kirk was left pondering as to what to do. After a few moments of this, he went to his communications console located at his work desk. He opened his private intercom channel. "Kirk to Security." He said once it was opened.

"Security, Lieutenant Rowe here…" came the voice of the Security Chief just seconds later.

"Lieutenant, I want you to gather half of your men and meet me in the Meeting Hall on Deck Two in fifteen minutes!"

"Acknowledged!" Lieutenant Rowe said.

Kirk then closed the intercom channel, and was left to wonder if he was doing the right thing.

* * *

_Captain's Log, Supplemental – Having just been informed by Princess Celestia that The Crystal Empire was being besieged by a changeling army being led by the evil tyrant King Sombra, I have asked Lieutenant Rowe, our Chief of Security, to gather half of his men in the Meeting Hall. Meanwhile, I am wondering if what I am about to do is really the right thing._

Captain Kirk was gripping the speech podium while facing the eighty-five men that made up half of the Enterprise's Security Force. He may regret what he was going to say next later on, as it goes against everything Starfleet has taught him about the Prime Directive; but he felt that it was "the only logical approach" as Spock was always so fond of saying.

"We'll be beaming down into the _heart _of the siege!" Kirk told his gathered men. "Which may escalate into full scale battle, if not all out _war! _

"You already know what the enemy looks like, so expect to face _many _of them, should they _attack! _You'll each be assigned a phaser with three additional power packs each. Set your phasers on Force Three to _kill! _These so-called _changelings _won't show us mercy, so why should we show it to _them!?_

"Hopefully, we'll come out of this with minimal casualties as we embark on a fight for freedom and…" Kirk almost said _democracy,_ but caught himself realizing that Equestria was a _monarchy. "…prosperity."_

He then turned to face Dr. McCoy, who happened to have joined them in the Meeting Hall. "Would you care to join us, Bones?"

"Me? I'm a _Doctor, _not a _soldier! _I'd much prefer staying up here to monitor our three patients all while continuing to work on developing a cure, with which were really _close, _by the way…"

Kirk smiled. "Good." He told the Doctor. Then he turned to face his men. "Are there any questions?"

All remained silent.

"All right!" Kirk said after a few moments. "To the Transporter Room, _dismissed! _And God speed…" He finished with a slight grin.

Everyone filed out of the room on their way to the Enterprise's Transporter Room.

* * *

Kirk had one more stop to make in his quarters before heading to the Transporter Room. He stood before the magic mirror and placed the call to Princess Celestia. Within moments, the form of Equestria's ruler appeared.

"Captain!" Celestia said happily. "Have you reached a decision?"

Kirk nodded. "I have! I'll be sending down eighty-five of my men to The Crystal Empire armed with phasers set to kill, which should be _more _than a match for changeling warriors carrying long spears…"

"Still, don't underestimate the changelings. They are _ruthless _creatures…"

"Don't worry, we won't! I also have a _plan _that I'll discuss with Shining Armour that will hopefully even the odds…"

"Very well!" Celestia said. "I also request that you bring Twilight Sparkle and the other wielders of the Elements of Harmony to the Crystal Empire. I have already given them their necklaces, and Twilight Sparkle already has her crown. As you well know, they've faced changelings _before, _so they know what they'll be up against. They'll be an _invaluable asset _in the coming fight! You have transportation technology that could make this possible, if I'm not mistaken."

Kirk nodded. "_Yes! _We'll beam them directly from Ponyville to the Crystal Empire. Mr. Spock is with them, so I'll have him beamed over as well."

"Go directly to the Throne Room of the Crystal Palace. I'll tell Princess Cadence to expect you there." Princess Celestia smiled. "You already have my eternal thanks!"

Kirk smiled and bowed. "You're welcome. It's the _least _we could do."

"You have already done more than expected! I wish you all the very best!"

Celestia's image faded from the mirror. Kirk then left for the transporter room. The double doors to his quarters SWISHed open to allow him out into the hall, and SWISHed close once he had left.

* * *

Minutes later, inside the Throne Room of the Crystal Palace, the warbling sound of the transporter beam could be heard as the form of Captain Kirk and the remainder of the Security Force accompanying him materialized.

"Greetings, Captain!" Princess Cadence said as she approached Kirk.

"Your Highness…" he said as he bowed before her. "Shining…" he then said, nodding to Shining Armour, who came to stand next to his wife.

"Welcome to the Crystal Empire, Captain…"

Before Kirk could respond, the sound of the Enterprise's transporter beam was heard again as more forms shimmered into existence. It was those of Mr. Spock, Twilight Sparkle and the other wielders of the Elements of Harmony; but there was someone else with them.

"Mr. Chekhov!" Kirk said as he came to stand before the young Ship's Navigator. "I don't recall inviting _you _to this party…"

Chekhov smiled slightly and shrugged. "You know _me, _Captinne. I've _always _been a _party crasher… _Besides, I want to help defend this Empire as much as anyone _else…"_

Kirk smiled at Chekhov's boldness. "All right. Just stay close to us…"

"CADENCE!" came an excited voice from Kirk's left.

"Twilight Sparkle…" said Cadence as both mares came to face each other.

"Get ready for it…" Shining armour whispered to Kirk.

"Hmm?" Kirk muttered in confusion.

Cadence and Twilight Sparkle then went into their familiar song and dance. _"Sunshine, sunshine! Ladybugs awake! Clap your hooves and DO A LITTLE SHAKE…" _Then they giggled joyfully and fell into each other's embrace.

"Oh!" Kirk said as he tried to hide his smile. "I guess that will always be their… _secret handshake… _will it?" he said to Shining Armour.

"Unfortunately!" Shining Armour said with a roll of his eyes. "As a colt, she even made me _do _it a few times… Long story…"

"Of course…" Kirk said.

Some of Kirk's men couldn't help but giggle at what they just saw.

Once this personal ritual she had with Twilight Sparkle was over, she cleared her throat and came to face Kirk and his men. "I'd like to officially welcome you all to the Crystal Empire. I and my husband wish to _thank _you from the bottom of our hearts that you are all _here _in answer to our call for help…"

Kirk smiled and bowed. "Our pleasure, Your Highness…"

"Since we're dealing with an enemy who is in possession of very powerful magic, I have something here that would help us _capture _him…"

She produced a simple looking cone shaped apparatus that was about five inches long and looked to be made of black rubber. Attached to it was a leather chin strap.

"It's called a _magic inhibitor…" _Cadence said. "Our guards use it on unicorn prisoners to dampen their magic abilities during incarceration. _This _one is imbued with a most powerful dampening spell. As soon as it's applied on King Sombra's horn, he'll be rendered _powerless._

"It will be up to _you, _Twilight Sparkle, to fit him with it…" she said as she used her magic aura to hand the apparatus to the young alicorn. "If he can be distracted long enough, it will make your task a lot easier…"

"But…" Twilight Sparkle started to object. "King Sombra's the most powerful unicorn we've ever _known…_ How can I distract him _and _put this magic inhibitor thing on him _at the same time!?"_

"Just leave the distracting to _us, _Twily!" Shining Armour smiled. "You do the rest…"

Twilight Sparkle still looked unsure.

"I know you can do it, Princess!" Cadence encouraged. "You just have to believe in yourself!"

Twilight Sparkle sighed. "Well, all right…"

She was given a saddlebag to put the magic inhibitor in. She slung it on her back after it was safely inside.

"_Now,_ Captain!" Shining Armour began. "I'd like to take you and your soldiers to the northern outskirts of the city so you can see what we're up against…"

Kirk nodded. "Of course! Lead the way…"

Shining Armour nodded, put on his helmet, and started leading them outside.

"Lieutenant…" Kirk began as he got beside the Chief of Security. "I'd like you and your men to stay close behind me and Mr. Spock…"

"Aye, sir…" Lieutenant Rowe said in response.


	7. Chapter 7 - Invasion

**CHAPTER 7**

**INVASION**

On their way to the northern part of the Imperial City, Shining Armour decided to brooch Captain Kirk about the "Alamo" subject.

"So tell me more about this… _famous battle_… you were talking about earlier…"

Kirk decided to let the Captain of the Royal Guard know everything he knew about it from the history classes he had. "This goes back to late 19th century Earth, which was a _long _time ago for us. A small group of a hundred and eighty or so men were defending the border of a State called 'Texas' from an invading Mexican army _thousands _strong.

"Few people gave them any chance of surviving the onslaught; but against all odds, they ended up _defeating _the Mexicans without the loss of a single life amongst them…"

Shining Armour smiled. "Seems like we're facing similar odds… But what does that phrase you said have to do with that 'famous' battle?"

Kirk smiled. "'Remember the Alamo' was a phrase that they coined to give themselves _courage. _It was actually a nearby _fortress _that was conquered by the Mexicans a few years prior. The small group of Americans defending that post all died at the hands of the invaders,but not before giving all they had in their fight for freedom…"

"Seems like we're about to have our _own… Alamo…"_ Shining Armour said.

"Let's hope not…" Kirk replied. "By the way, I've thought of a _strategy _on how we can hopefully even the odds a little bit…"

"Let's hear it!" Shining Armour said.

"If that changeling army _attacks, _I want you and your men to _draw back…"_

"Men?" Shining Armour said in confusion.

"Uhh… _males…" _Kirk replied, realizing his misnomer.

Shining Armour smiled. "We do have a few _mares _serving amongst our ranks…"

"_Ponies, _then!"

Shining Armour chuckled. "Just _soldiers _is fine, Captain… or _troops… _But how does _falling back _help even the odds?"

"You know these city streets, they _don't… _You can lead them down narrow alleyways and dead ends where they'd be _easy pickings… _It'll be like classic _urban warfare…"_

After pondering it for a few moments, Shining Armour nodded. "Makes a lot of sense… I'll let my… _men… _know…" He said with a smile, using Kirk's vernacular.

Kirk couldn't help but chuckle at this.

They finally arrived at where the Pony Army was stationed. Even though they were less than three thousand, they still looked many in number.

Shining Armour got the attention of a Lieutenant, who trotted over. "How's everypony doing?" he asked.

"Not good, sir!" the Lieutenant replied. He was a dark grey unicorn stallion with light blue coloured mane and tail. "A whole bunch had to be dismissed just an hour ago to report to Medics because they came down with this… _disease…"_

Shining Armour looked worried. "How many are left?" he asked reluctantly.

The Lieutenant frowned. "Just over twenty five hundred, sir…"

"_Dammit!" _Shining Armour exclaimed under his breath. "What about the enemy?"

"They haven't budged, sir…" the Lieutenant reported. "Their envoy is due back any minute now for the answer to their ultimatum…"

Shining Armour nodded. "All right, Lieutenant. Carry on…"

The unicorn stallion saluted before returning to his post.

"Brace yourself, Captain! You may not like what you're about to see…" Shining Armour told Kirk as he moved towards the front of the Royal Guard's ranks.

"Stay here!" Kirk told Lieutenant Rowe and his men as he moved to follow Shining Armour.

Shining Armour squeezed through the soldier lines to get to the front. Kirk stayed right on his tail. As he glanced among the assembled ponies, he could see the great fear in their eyes. He even saw a couple of mares with visible equine fear showing on their facial features. This told him that Shining Armour wasn't lying when he said that there were females serving in their ranks.

When he got to the front of the lines, he was greatly surprised by what he saw! Stretching from one end of the city limits to the other, it seemed, was a huge dark grey mass! Kirk knew already that the Changeling Army counted twenty thousand members, but he had no idea of the sheer volume of space an army twenty thousand strong could occupy! They were about a kilometer away; but even at that distance, they looked like they could _easily _overrun the Royal Guard defences and engulf the Imperial City! Compared to a resistance force of a little over twenty five hundred, the odds seemed quite overwhelming _indeed!_

"You were _right, _Shining! I _should've _braced myself…" Kirk admitted.

"Told ya!" Shining said in reply.

Then they saw the shape of a dark grey changeling trotting towards them.

"Here he comes…" Shining Armour said.

Kirk knew right away that this was the envoy being sent by Sombra for the response to his ultimatum of unconditional surrender. As he got closer, Kirk thought he recognized who this changeling was, but he wasn't sure.

As the changeling unicorn approached, Kirk finally recognized who he was: It was the same changeling who was in his cell with Sombra that day he was interrogated. He deduced that it was probably the same changeling who knocked him out in Ponyville and took him through the magic porthole in the Everfree Forest to King Sombra's dungeon hideout.

As the changeling known as _Hugh _came within a few feet in front of the Royal Guard's lines, he stopped. He was wearing dark grey armour with a dark crystal symbol on the chest plate, and a simple steel helmet. He also had an insignia on his shoulder plates identifying him as a high ranking officer.

His eyes narrowed as he saw who was standing next to Shining Armour. "Tiburon Tamer…" he growled.

"That's what you knew me as, but my _real _name is James T. Kirk, Captain of the U.S.S. Enterprise, representing the United Federation of Planets!"

Unaffected by this, Hugh turned his attention to Shining Armour. "My Master is awaiting your response. Do I have your unconditional surrender?"

Before Shining Armour could answer, Kirk levelled a finger at Hugh. "You tell Sombra that if he attacks this city, he'll be in for a _fight! _I have eighty-five men armed with phasers set to kill, which is _more_ than a match for whatever weapons you carry! We're not about to let you and your army waltz into the Crystal Empire without any resistance!"

"He's _right!" _Shining Armour said. "We'll _never _surrender!"

Hugh smiled wickedly. "Very well!" He then turned and trotted back towards the changeling army.

"I think they're going to attack…" Shining Armour said.

I couldn't agree more…" Kirk said in response.

* * *

Meanwhile, in Sick Bay on board the Enterprise, Dr. McCoy was preparing a hypodermic injector containing the prototype of a vaccine he developed using serum from Apple Bloom's blood.

"Do you really think it will work, Doctor?" Nurse Chapel asked him.

"Only one way to find out!" Dr. McCoy said.

He moved to Sweetie Belle's bedside, and pressed the hypo against her left foreleg. The injector HISSed as it delivered the vaccine into the young filly's bloodstream. He then grabbed his medical tricorder and began to take readings. It warbled as he scanned Sweetie Belle's body with it.

After a few seconds, he smiled. "It's _working!" _he cried. "The vaccine's _taking effect!"_

Nurse Chapel sighed in relief. "Well _that's _good news!" She smiled.

"Prepare a dose for Scootaloo, and tell the Lab to start mass producing it for the planet's population." Dr. McCoy ordered.

"Right away, Doctor!" Nurse Chapel said happily.

McCoy then moved to stand by Apple Bloom's bedside. "And how's my _healthiest _patient doing?"

"Just fine, Doc!" Apple Bloom said as she looked up from the book console in front of her. "Ah gotta say ah like this here _Little Red Ridin' Hood _book ya gave me, but ah _don't _like the part where the grandmother gets eaten by the _Big Bad Wolf…"_

Dr. McCoy smiled. "Not every kid _does… _I know I didn't! Even gave me _nightmares _for awhile…"

"Really?"

McCoy nodded. "I must say you're a _really special filly, _Apple Bloom! The antibodies in your blood are quite _different _than… anyPONY else… which explains you haven't actually gotten _sick _from the disease."

"Told ya it was that Apple family resilience!" Apple Bloom smiled.

McCoy smiled back. "I don't doubt _that…"_

Nurse Chapel came back and handed McCoy a fresh hypo containing the vaccine for Scootaloo. "STILL, I'd like to give you a _milder _form of the vaccine, just in case. Can't have you spreading the disease around until everyone is immunized…" McCoy said.

"Well all right, if ya say so…"

He then moved to Scootaloo's bedside and injected her with the vaccine. He then scanned the young Pegasus filly for a few seconds before closing his medical tricorder. "There!" he said with satisfaction.

"Keep them under observation, and let me know if they relapse…" McCoy told Nurse Chapel.

"Yes, Doctor." Nurse Chapel said with a nod.

McCoy then turned to leave Sick Bay.

"Where are you going?" Nurse Chapel questioned.

"Where I think I'll be needed the most…" He told Chapel before walking through the double doors of Sick Bay and into the hall.

* * *

Captain Kirk came out of the rear lines of pony soldiers to stand next to Lieutenant Rowe and the Security Force. "An attack is imminent! Prepare yourselves for the onslaught…" he told the Lieutenant.

Lieutenant Rowe glanced back at assembled Security Team in red shirts. "My men are ready, sir!"

He then turned his attention to Twilight Sparkle and her friends. "Well, ladies! Looks like we're about to face a changeling invasion. Hope you're ready for it…"

"Hey, don't worry about _us…" _Rainbow Dash said as she hovered in mid air. "We've dealt with changelings before. We'll show THEM who's boss!"Still hovering, she made a punching motion with her forehooves.

The warbling sound of the transporter beam made everyone turn. Just a few feet away, the form of Dr. McCoy slowly materialized into being.

"Bones!" Kirk said in astonishment. "What are _you _doing here!?"

"Great news, Jim! I've developed a vaccine that actually _works! _I've administered it to Sweetie Belle and Scootaloo, and they're actually getting _better!" _

Rarity let out a breath. "Thank _goodness! _I was SO worried!" she said as she placed a forehoof to her forehead.

"That _is _great news! How'd you do it!?" Kirk asked.

"It was actually the antibodies in Apple Bloom's blood that did it! She has an extremely rare immunity to certain viruses, _including _this new strain!"

"Ah always _knew _that little filly had it in her!" Applejack said with pride.

"Well done, Bones!" Kirk smiled as he patted McCoy on the shoulder. "But that doesn't explain why you're _here…"_

"Well, I'm here to volunteer my services as a _Field Medic. _As primitive as pony medicine is, I figured they could use someone with a little bit more knowledge of _advanced _medical techniques…"

Kirk smiled and motioned towards a Pony Medic he could consult with. McCoy rapidly went to join him.

The sound of a huge war cry and the rumbling of the ground then came over them. The changeling army had begun their charge! In just a few minutes, they'll be right on top of them!

"Here we go…" Kirk muttered over the din of charging changeling army.

The changelings stampeded headlong towards the Imperial City, long spears at the ready. Their deafening war cry was enough to make _anypony _shiver out of fear. Within minutes, they were two hundred lengths from the entrance to the city, and the Royal Guard.

"FALL BACK!" Shining Armour shouted. Almost as one, the entire Royal Guard turned on their heels and started galloping into the city.

"Fall back NOW!" Kirk shouted to his men, who immediately turned and followed the ponies' lead as they ran towards the center of the city.

While the ponies of the Royal Guard scattered, Kirk and his men stayed in one group as they continued to run towards the downtown area of the Imperial City. After they ran five hundred feet, they stopped.

"Form a line!" Kirk ordered, and all of the Security officers came to stand side by side.

"Ready phasers!" Kirk then ordered. Everyone drew their phasers.

By this time, the changeling army was already galloping into the city, their war cry drowning out every other sound. Those changelings that happened to be Pegasi took to the air. They were soon met by the Royal Guard Pegasi, and began their aerial combat.

"FIRE AT WILL!" Kirk shouted when he felt the charging changelings were close enough.

The buzzing sound of eighty five phasers reverberated as they shot their red beams of light at the charging changelings. Several fell dead under the blast of the laser beams, but it seemed to barely make a dent in the approaching mass of changelings. Kirk's men fired again, and took out several more changelings.

It wasn't long before Kirk's men had to break rank and scatter, or else they'd been taken out by the changelings themselves. It was here that they turned the fight into the deceptive art of urban warfare.

The ponies of the Royal Guard did the same thing. They scattered every which way, hoping to lure some of the changelings into the narrow streets and alleyways of the Imperial City where they would be easier to fight.

Twilight Sparkle and her friends fought hoof to hoof against the charging changelings. While Twilight and Rarity used their magic powers to shoot lightning bolts at the changelings charging them, Applejack used her bucking technique to take out any changeling who came near her, like she was bucking apple trees back at Sweet Apple Acres. Rainbow Dash, being a Pegasus, took to the air to join in the aerial combat with the Royal Guard Pegasi against the winged changelings. She mostly used her forehooves to fight the approaching changelings boxing style. Pinkie Pie tried using some pony martial arts techniques Rarity once taught her, but soon realized that this was ineffective; and resorted to slapping them silly before knocking them out with a solid right hoof. Fluttershy decided to join Dr. McCoy and the other pony Medics to help treat the wounded, which were already numerous. She stayed close to Dr. McCoy the whole time.

Meanwhile, King Sombra was walking very confidently down the main street of the Imperial City. He had a wicked smile on his facial features. He used a lightning spell to repel back any Royal Guard pony who tried to attack him. The pony guards screamed as they flew through the air, and were silenced as they landed on the hard surface of the street. He soon found his intended target, and slowly approached.

Twilight Sparkle was fighting off changeling after changeling; but it seemed that for every changeling she took out, two more were right there to take his place! She was finally able to break through a charging line, and soon found herself facing a familiar wicked grinning foe.

"King Sombra…" she growled as she assumed her defensive stance.

"Twilight Sparkle! We meet again!" Sombra said in his deep menacing voice. "Last time we met, I _told _you I would get my _revenge! _Have you ever heard the old proverb that says 'revenge is a dish that is best served _cold'_? Well, it's VERY cold in space; and that's where I will _send _you once I'm _through _with you!"

"Not if I can help it!" Twilight Sparkle growled.

Sombra smiled and humpfed. "So be it!" He then began to power up his magic to deliver the death blow.

Twilight Sparkle called forth her own magic in a repulsion spell.

The dark purple aura of Sombra's evil magic shot forth from his horn directly at Twilight Sparkle. The aura of Twilight Sparkle's own magic worked to counter Sombra's spell as both auras collided in an explosion of light between them. It wasn't long, however, before Sombra's spell seemed to overtake Twilight's. Twilight Sparkle's face contorted in a weird expression as she struggled to keep her spell working while Sombra grinned evilly as he maintained his own spell with seemingly little effort. Finally, in an explosion of light only a few inches in front of her, Twilight screamed as Sombra's spell finally broke her counter spell, and sent her flying through the air. After flying twenty feet, she fell hard to the ground and almost lost consciousness.

The explosion of light drew the attention of everypony nearby. Among them was Shining Armour. When the Captain of the Royal Guard noticed that it was his little sister who was just felled by King Sombra, his eyes grew wide. "TWILY!" he shouted. Overcome by anger at what he had just seen, he grabbed a long spear and charged headlong at Sombra, letting loose a war cry. Sombra closed his eyes as he concentrated, and called forth a protective shield around himself. Shining Armour grunted as he was pushed back by the shield.

Meanwhile, Rainbow Dash also saw the explosion of light from where she was in the air. When she saw that it was her friend Twilight Sparkle who had just fell to King Sombra, she gasped. "TWILIGHT!" she cried. Then, in a fit of rage, she started to go into a nose dive charge towards King Sombra. She accelerated quickly as she extended her right forehoof, ready to strike. She screamed as she ran into the wall that was King Sombra's protective shield spell, and found herself getting blown back. She rolled for several feet once she hit the ground, and finally stopped stretched out on her belly groaning in pain.

Meanwhile, in another part of the city, Captain Kirk, Mr. Spock, Mr. Chekhov and Lieutenant Rowe had taken cover behind the concrete wall of the entrance to a building, and were fighting off the continuous stream of charging changelings.

"There's too many of them, Captain!" Mr. Spock shouted over the din of battle. "We can't hold out much longer!"

"We have to TRY, Spock!" Kirk replied as he shot another phaser blast at a charging changeling, killing him instantly.

Then he saw the horrific sight of one of Lieutenant Rowe's red shirted men get taken down from behind by a changeling. The man's scream could be heard as the changeling bit into his neck. The Ensign died seconds later. Then he saw another red shirted Ensign take a long spear through the back as he tried to run from a changeling who had overpowered him. The Ensign died instantly as the long spear pierced his heart.

Kirk pressed his lips as he fought back the emotions of seeing two of his men die before his very eyes and fired his phaser at any changeling in sight.

"CAPTINNE!" Mr. Chekhov, standing beside him, shouted to get his attention. "My phaser's almost out of power, and I'm down to my LWAST power pack!"

"Me, too!" Lieutenant Rowe, who was standing next to Chekhov, also admitted.

"We've got to keep _fighting, _men!" Kirk said resolutely. "The fate of this entire civilization _depends _on it!"

Seeing their Captain's resolve in the matter, they both continued firing their phasers. Kirk and Spock did the same thing.

Spock was even forced to use his Vulcan neck pinch on a changeling who had appeared on their right and somehow dodged a phaser blast as it jumped over the concrete wall. The changeling fell to the ground unconscious before he could deal a death blow to Captain Kirk.

Twilight Sparkle was having her own problems with King Sombra. She moaned as she slowly opened her eyes. She could hear Sombra's evil laughter as he slowly approached her prone form lying on the ground. She looked up and saw his grinning face gaze down at her.

"You're _finished, _Twilight Sparkle!" he told her. "Surrender to me _now, _and I will let you _live!"_

"I'll _never _surrender to you!" she growled at him.

King Sombra smiled wickedly. "Very well!" he said. His horn glowed with his magic aura as he called forth a death blow spell, and prepared to strike Twilight Sparkle with it.

However, nopony noticed that another army approached the Imperial City from the southwest. This was an army that could easily match that of King Sombra's army, and it was made up exclusively of _changelings. _They were being led by a lanky looking female changeling who was six feet tall, not including her twisted horn. She was dark grey in colour a long flowing teal coloured straight mane and tail that were pock marked with holes. Her legs also had holes in them, but she was still able to stand straight on them. This was _Queen Chrysalis, _and she had gathered an army that marched all the way up to the Imperial City of the Crystal Empire.

"ATTACK!" she shouted as she pointed her right forehoof in the direction of the downtown district. Everypony nearby cringed in fear as the changelings charged headlong, both on the ground and in the air, into the fray.

"Changelings _only!" _she shouted to her troops as they charged. It was here that everypony realized that her army was here to combat King Sombra's army, and not the crystal ponies. This renewed the resolve of the remaining soldiers of the Royal Guard as their sense of doom soon disappeared, and they found new energy to keep fighting.

While her army was busy capturing or killing any of King Sombra's changelings who resisted, Queen Chrysalis made her way to where Sombra was located. She had only one purpose in this entire affair, and she was determined to see it through.

The sound of Queen Chrysalis' invading army caused Sombra to interrupt his death blow spell and turn to see this unexpected turn of events. "What!?" he exclaimed as he saw numerous changelings attacking his own.

He was in a general state of confusion as to what was going on until he saw the slender form of Queen Chrysalis approach him with a look of determination in her eyes as she zoned in on him.

"What is the meaning of THIS!?" King Sombra exclaimed as Queen Chrysalis stopped a few feet away from him.

"King Sombra, you have _illegally _acquired changeling material and know how to create this _army _of yours; and for _that, _you must PAY!"

She then called forth a combat spell to fight King Sombra. King Sombra called forth a counter spell of his own. Both of their auras met in the middle in an explosion of dark light as they collided. Both of them made a face as they fought with all of their might to combat each other on the magical plain.

In the meantime, Twilight Sparkle was slowly coming to her senses. Upon seeing that King Sombra was distracted, she seized the chance! She used her alicorn magic to take the magic inhibitor she was given out of the saddlebag she was carrying, took to the air and hovered above King Sombra, and aptly placed the magic inhibitor around King Sombra's horn and quickly tied the chin strap in place.

"WHAT!?" King Sombra exclaimed as he felt the inhibitor being placed upon him, then screamed as he fell to the ground under Queen Chrysalis' attack spell as his own magic dissipated. Once King Sombra was lying flat on the ground, she released the spell.

Shining Armour, witnessing this, instantly knew that King Sombra was no longer a threat. He motioned for two of his nearby soldiers to seize King Sombra. Then he went to check on his sister, who had just returned to the ground.

"You okay, Twily?" he asked as he placed a hoof to the small of her back.

"None the worse for wear…" said a smiling and battered Twilight Sparkle weakly.

Shining Armour smiled with the notion that his baby sister was okay.

Meanwhile, all of Queen Chrysalis' changelings captured King Sombra's changelings, and gathered them all in a huge circle not far away from where the Crystal Heart normally stood. Those of King Sombra's changelings that still resisted had to be killed! The battle was _over, _and King Sombra had _lost!_

Princess Mi Amore Cadenza, who had been taken away to safety in an underground bunker, re emerged once the battle was over, and made her away to the central part of the city where everypony else was gathered. The elite guard assigned to protect her formed a protective circle around her.

All tolled, nearly half of King Sombra's army were killed or injured. The rest were captured and brought to that huge makeshift circle. Twenty-five of Captain Kirk's Security Force were killed or injured while nearly fifteen hundred of the Royal Pony Guard suffered the same fate. It was thanks to Queen Chrysalis' changeling army, which lost only a few members, that the day was won!

Twilight Sparkle and the other wielders of the Elements of Harmony suffered a few bumps and bruises, but didn't incur any major injuries.

"Queen Chrysalis…" Princess Cadence said to get her attention.

Queen Chrysalis, who was still directing traffic, turned at the sound of her name.

"You have done a great service to us today by helping us defeat King Sombra's army; and for _that, _you have our eternal gratitude!" Princess Cadence said as she bowed.

Queen Chrysalis' eyes squinted as she glared at her. "Do not think that you have gained an ally here today, _Crystal Princess! _I still intend to take over Equestria someday. It's just that my plans of conquest don't include HIM!" She pointed to King Sombra, who was still struggling against the three pony soldiers holding him.

"Take him to the Palace Dungeons and put him in solitary confinement!" Shining Armour ordered.

The three pony soldiers saluted and dragged the still struggling King Sombra away.

"Let me go!" came the cry of a familiar voice.

Two changelings burst through the crowd carrying a struggling member of King Sombra's army to stand before their Queen.

"AH! Third of Five, we meet again!" said an evil grinning Queen Chrysalis.

The changeling before her breathed heavily through his nose. "How many times do I have to tell you my name is HUGH!" he said angrily.

"Irrelevant!" Queen Chrysalis said as she glared at him. "That designation will disappear once you are a part of _us _again! Same as these other changelings you've helped create…"

"What's gonna happen to them?" Captain Kirk asked.

"Who are _you?"_ Queen Chrysalis asked.

"James T. Kirk, Captain of the Federation Starship _Enterprise!"_

Chrysalis smiled evilly at him. "Charmed, I'm sure! It's quite simple, _Captain, _these changelings will be assimilated into our Collective. We will add their distinctiveness to our own as they become a part of the Hive Mind."

"And losing all individuality in the process?"

Chrysalis nodded. "That is the end result of assimilation, yes. But that is _not your concern, _or that of the Crystal Empire!"

Captain Kirk stayed silent knowing he was not going to win this argument with her, but he never took his eyes off of her as he still glared at this sinister Changeling Queen.

Chrysalis turned her attention back to Hugh. "You are no doubt wondering how we learned of what you were doing here. It was quite simple, really! We had a double agent infiltrate your group of defectors. It was thanks to him that we were able to get wind of Sombra's sinister plan…"

The double agent in question came to stand next to Chrysalis. He smiled evilly at Hugh. Hugh recognized him as one of his Sub Lieutenants whom he trusted greatly. He even came to value him as a close friend! Hugh glared angrily at the changeling male who betrayed him.

"Seven of Nine, Six of Nine… put him with the others…" she ordered the two guards holding Hugh. They saluted and began to drag him towards the circle of changeling prisoners.

"NO!" Hugh cried as he struggled against their grip. "I won't go back!" He managed to break free of the guards' grip and began to run away.

"HEY!" Shining Armour shouted as he came forward. He bent his head down and shot a lightning spell in the direction of the escaping Hugh.

Hugh screamed as the lightning bolt hit the back of his neck. He collapsed to the ground with a black smoldering wound right where the lightning bolt hit him.

Dr. McCoy immediately rushed to the aid of Hugh. Captain Kirk, Shining Armour and Twilight Sparkle followed close behind. As the crowd gathered, Dr. McCoy bent down and checked Hugh's neck for a pulse.

"He's _dead, _Jim!" McCoy told Captain Kirk sadly.

"Was that really necessary?" Twilight Sparkle asked Shining Armour with one forehoof upraised.

"He left me no choice, Twily!" Shining Armour said evenly.

Twilight Sparkle had never imagined that her big brother to be one to kill another pony, even a changeling; yet here was one lying on the ground before her, a victim of her big brother's hooves. She figured he must've been forced to kill a few changelings during the heat of battle, but she couldn't say that she was a witness to these events. This was a side of her big brother that she really didn't like!

Queen Chrysalis' magical aura surrounded Hugh's body as he was lifted from the ground and dragged away. "It is a great loss" Chrysalis unemotionally admitted. "for he was an _excellent _drone…" She left Hugh's body to the care of her two guards, who used their own magic to carry him away. "He will be remembered, don't you worry…"

Then she turned to face Twilight Sparkle. "_Now, _we must take these changeling prisoners back to The Badlands _quickly, _and I know no quicker way than through the magic of you and your friends' Elements of Harmony; which is why I call upon _you, _Princess Twilight Sparkle; and your friends, to use your magic to send us _home…"_

Twilight Sparkle looked questioningly at Queen Chrysalis. "But… are you _sure _about this!?" she asked with one forehoof upraised.

Chrysalis nodded. "I'm sure… Now, _please…"_

Twilight Sparkle sighed. "All right… Get ready, girls!" she then told her companions as they gathered around her.

"'Til we meet again, Crystal Princess!" Chrysalis told Cadence as she grinned evilly.

Cadence's eyes grew wide as she wasn't sure whether or not to take Chrysalis' threat seriously.

Twilight Sparkle and the other wielders of the Elements of Harmony closed their eyes as they concentrated. As their magic built up, the Earth ponies Applejack and Pinkie Pie started to slowly levitate off the ground. After they reached a few feet off the ground, they stopped and hovered there. Applejack was to Twilight's right, and Pinkie Pie to Twilight's left. The two Pegasi Rainbow Dash and Fluttershy used their wings to hover just above the two Earth ponies. Rainbow Dash was to the right and Fluttershy was to the left. The unicorn Rarity hovered just above Twilight Sparkle about half a foot below Rainbow Dash and Fluttershy.

Contrary to the last time they used their Elements of Harmony, their formation wasn't in the shape of a six point star, but of a _heart; _for _now, _not only was the magic of friendship a part of their Elements' power, but that of _love _as well!

"ALL HOOVES, BRACE FOR IMPACT!" Queen Chrysalis called out, sending that the blast from the Elements of Harmony was imminent.

When the power of their magic had built up enough, Twilight Sparkle opened her eyes, and out shot a tremendously huge flash of light that exploded in front of Queen Chrysalis and the gathered changelings. The flash of light expanded all around and blew back the changelings, and sent them flying through the air. Since they had their backs turned towards the southwest, which was the direction of The Badlands, that was where they would be sent back. The victory of the crystal ponies was complete!

For the rest of the day, and all throughout the night, the crystal ponies celebrated the victory! Not only were they once again freed from the menace of their all time greatest enemy, but they managed to capture him and lock him away in the Palace Dungeons. Fireworks went off here and there and great revelry took place as the crystal ponies pulled out all of the stops in their festivities! Captain Kirk and his surviving men were invited to partake in the celebrating. Kirk, not wanting to miss an opportunity to be a part of a grand celebration, gave his men permission to be festive for the night!

Shortly after midnight, the crystal ponies slowly began to stagger home to sleep off their evening of wild partying. This was the cue for Captain Kirk and his men to beam back up to the Enterprise and head for their own respective quarters to sleep off their own wild night of partying.


	8. Chapter 8 - Aftermath

**CHAPTER 8**

**AFTERMATH**

_Captain's log, Star Date 5194.2 – It's been seven days since the battle between King Sombra's Army and the combined forces of my own men and the ponies of the Crystal Empire. After that hard fought victory, Dr. McCoy instituted a planet wide vaccination program to combat the Vegan Chorial Meningitis strain that has been plaguing the inhabitants of Equestria. The inoculation program was a huge success, and the disease is now in full remission._

_On the eve of our departure, Princess Celestia has invited myself and all of my crewmembers who participated in that fight for freedom down to the Palace of the Imperial City for a special ceremony._

Captain Kirk was standing in front of the small dresser mirror in his quarters, putting the finishing touches on his dress uniform. The buzzing sound of the doorbell from the entrance to his quarters told him that someone was outside looking to get in. "Come…" he said.

The double doors SWISHed open to reveal Dr. McCoy. The double doors SWISHed close as soon as he walked in. "Are you ready?" the Doctor asked as he came to stand next to Kirk.

"Almost…" Kirk said as he continued with his final grooming.

"I _hate _having to wear the dress uniform!" McCoy complained. "I feel like I'm about to _choke _to death…" He used a finger to momentarily pull the collar of his dress shirt away from his neck.

"Princess Celestia specifically asked for it, so there must be a _reason…" _Kirk smiled and shrugged.

"Well, no doubt it's to… _congratulate _us on a job well done. But didn't she also say that there would be a 'little surprise' waiting for us?" McCoy asked.

"She _did…" _Kirk smiled.

"Another stained glass window done in our honour?"

"We'll find out when we get there…" Kirk shrugged again as he started to leave his quarters.

The double doors SWISHed open to let both men out, and SWISHed close behind them once they left.

Minutes later, in the hallway of the Crystal Palace just outside the Throne Room, the warble of the transporter beam could be heard as the forms of Captain Kirk, Mr. Spock, Dr. McCoy and Lieutenant Rowe, the Enterprise's Chief of Security, materialized into being.

The sixty surviving members of the Security Force who participated in the battle against King Sombra's Army seven days prior had already beamed down and were waiting for the arrival of their leaders.

Twilight Sparkle and her friends, the other wielders of the Elements of Harmony, were also present and were chatting with some of the Enterprise's Security Officers. They wore the same outfits they had at Twilight's recent coronation. Twilight Sparkle herself looked particularly regal in her pink and white dress with yellow trim and white bows, gold coloured hoof shoes emblazoned with her six pointed star cutie mark symbol. She also had her Princess' crown on her head.

"Welcome to the Crystal Palace, gentle…_men…" _said a dark yellow coloured male Earth pony with dark blue mane and tail as he came to greet them. He wore a gold coloured suit of armour with matching Roman style helmet.

Kirk bowed to the Earth pony. "I thank you… uhh…"

"Oh! Flash Sentry, sir…" the Earth pony replied.

"You're new here, aren't you?" McCoy asked.

"Yes, sir!" Flash Sentry smiled and nodded. "My garrison was one of the two who were transferred here from Canterlot as reinforcements after the battle…"

This was true! Since the Royal Guard Unit assigned to the Crystal Empire lost a thousand of its members during the fight against King Sombra's changeling army, two units were sent from Canterlot to replace them. Prince Shining Armour also launched a recruitment campaign among the crystal pony population, which was most successful. Captain Kirk figured that this young Earth pony must be the Usher who will lead them into the Throne Room.

Flash Sentry turned his attention to the gathered crowd. "Is everypony ready!?" he asked.

"So are _we…" _Dr. McCoy said realizing that Flash Sentry said "every_pony" _rather than "every_body"._

Flash Sentry smiled at the Doctor, but said nothing. "Follow me!" he said as he motioned for the two guards at the foot of the huge double doors leading to the Throne Room to open them.

Trumpets resounded throughout the huge expanse of the Throne Room as the entire party walked in. At the Throne sat Princess Celestia- the ruler of all Equestria, her younger sister Princess Luna, Princess Mi Amore Cadenza and Prince Shining Armour, her husband and Twilight Sparkle's older brother.

Princess Mi Amore Cadenza, or "Cadence" as she's better known as, was wearing the same dress she wore at Twilight's coronation, which consisted of a light blue dress with purple trim made to mimic a crystal pattern. Her mane was tied in a bonnet. Shining Armour wore the bright red blazer with gold coloured collar and cuffs that once belonged to his father. He also had a light blue sash running from his right shoulder and was criss-crossed over his chest.

Flash Sentry led the party up to about twenty feet in front of the Throne. Then he cleared his throat and spoke in a voice loud enough to be heard throughout the Throne Room. "Announcing Princess Twilight Sparkle, the other wielders of the Elements of Harmony; as well as Captain James T. Kirk of the U.S.S. Enterprise and company!" he said as he waved his left forehoof at them.

Princess Twilight Sparkle and Captain Kirk, being the leaders of their respective groups, approached the throne. Twilight Sparkle, being distracted by the lavishness of the Throne Room, accidentally bumped into Flash Sentry. "Careful there…" Flash Sentry said, smiling.

Twilight blushed as she smiled embarrassingly. "Sorry…" This caused a few members of the gathered crowd to giggle.

Captain Kirk and Twilight Sparkle stopped ten feet away from the Throne Room and bowed before the assembled Royals. All four Royals returned the bow.

Princess Celestia then stood up and walked over to the foot of the Throne platform, her hooffalls echoing on the marble floor of the platform. Captain Kirk looked up at her and all of her magnificence. He had forgotten how tall she really was! At six foot two, he was pretty tall himself; but even he seemed like a dwarf standing next to the six foot eight tall pure white alicorn Princess; seven foot five, if you included the alicorn's horn on her forehead.

"My dear friends…" she began. Her voice sounded soft and motherly. "On behalf of myself and my fellow Royals, I would like to officially welcome all of you to the Crystal Palace, home of the Crystal Empire…"

A smattering of applause from the gathered resounded throughout the Throne Room.

"Princess Twilight Sparkle…" she began after the applause had died down. "Once again, you and your friends, the wielders of the Elements of Harmony, have done us all a great service by helping our valiant troops defeat an invading tyrannical army and restoring peace to the Crystal Empire once more.

"Not only that, you yourself were instrumental in helping those same troops capture a ruthless enemy that has been a thorn in me and my sister, Princess Luna's, side for thousands of years. For all this, you and your friends have our eternal recognition and gratitude!" She bowed.

"On behalf of myself and my friends, I thank you, Your Highness…" Twilight Sparkle said as she returned the bow.

Another smattering of applause, slightly louder this time, reverberated throughout the Throne Room.

"Captain James Tiberius Kirk…" Princess Celestia continues. "You and your shipmates' aid in our time of great need shall be remembered for all eternity. Your exploratory nature has brought your space faring people and _my _people together in a bond of everlasting friendship. For that, you have our eternal thanks and _gratitude!" _She bowed again.

"On behalf of myself and that of my shipmates, I thank you deeply, Your Highness…" Kirk said as he returned the bow.

This brought more applause from the gathered crowd.

"I now turn things over to Princess Mi Amore Cadenza of The Crystal Empire for the delivery of our 'little surprise'". Princess Celestia said as she retreated back to her original place on the Throne's platform.

Princess Cadence then came forward. "My dear friends, as a token of our and the inhabitants of the Crystal Empire's appreciation for all that you have done, and your accomplishments, over this past week, we would like to bestow upon _all of you _a Medal of Valour embossed with our most sacred symbol, The Crystal Heart."

Thunderous applause resounded as Princess Mi Amore Cadenza herself came before each of Captain Kirk's men and personally pinned the medal on the chest of their dress uniforms using her alicorn magic. Each man bowed respectfully as they accepted the medal. The medallions themselves were made of pure gold; and, as Princess Cadence herself said, were embossed with The Crystal Heart effigy.

Captain Kirk and Twilight Sparkle were the last to accept the medal. As the leaders of their respective groups, they were the most important recipients of all. Kirk graciously bowed as the medal was pinned on his chest. As Twilight Sparkle accepted her own medal, Shining Armour came to stand beside his wife.

"I'm so _proud _of you, Twily!" Shining Armour said as he hugged his baby sister.

"Thanks, Shining!" she said as she accepted the hug. Then she noticed something on her big brother's face. "More _liquid pride?"_ she asked tenderly.

"Y-you know it…" Shining Armour sniffed as used his hoof to wipe the tear that fell down his right cheek.

"Awwwww… The big brave Prince is _crying!" _Rainbow Dash teased.

Applejack put her hoof to her mouth to stifle a giggle. Captain Kirk did the same with his own hand to his own mouth.

Twilight Sparkle and Shining Armour shared a laugh.

"Congratulations, Twilight!" Princess Cadence said as she hugged the mare she once foalsat as a filly.

"Thanks, Cadence!" Twilight said as she accepted the embrace.

Then Cadence moved back up to the platform of the Throne and cleared her throat. "ORDER!" Flash Sentry called out, as the crowd was still applauding, and there was widespread chatter here and there.

As soon as the crowd quieted down, Cadence spoke again. "I now direct your attention to the far right corner of the Throne Room…" she motioned. Everybody turned in the direction that the Crystal Princess was pointing to.

Trumpets resounded as a huge tapestry nobody had noticed before was unrolled. Some of the crowd gasped in astonishment as it was unveiled.

"Let this _wonderful _tapestry designed by some of our most skilled weavers serve as a memento of everything that has transpired here over the past seven days in The Crystal Empire , and all throughout Equestria, _for all time!" _

Trumpets resounded again as the crowd erupted in thunderous applause. It was, in fact, a beautiful tapestry weaved in brilliant colours that had Equestria's sun at the very top left and Equestria's one moon at the very top right with a likeness of Princess Celestia and Princess Luna below each respective celestial bodies marking them as the Sun and Moon Princesses. Below that, in the center, was the likeness of the starship Enterprise based on previous descriptions from Chief Engineer Scott. Below that was the skyline of the Crystal Empire's Imperial City. Below that was a scene on the left hand side that showed Captain Kirk, Mr. Spock, Ensign Chekhov, Lieutenant Rowe and a few red shirted Security Officers firing their phasers at approaching changeling soldiers. One red shirt even fired his phaser at a winged changeling flying through the air! On the right hand side was the image of some Royal Guard pony soldiers engaged in hoof to hoof combat with other changeling soldiers. There were even Pegasi soldiers engaged in aerial combat with winged changelings in mid air! Underneath this showed Dr. McCoy inoculating a pony with his hypo against the Vegan Chorial Meningitis disease with several other smiling ponies waiting in line for their turn to be inoculated. There were even Pegasi and unicorns standing in line, as their horns and wings could clearly be seen! This served as a symbol of Equestria's diverse pony population. There was even an Earth pony mare carrying her infant foal waiting for their turn to receive the cure! At the very bottom of the tapestry was the likeness of The Crystal Heart with an effigy of Princess Cadence on the left and Prince Shining Armour on the right wearing the exact same outfits they wore today.

"I expect your volume recounting the entire events by the end of the week, Twilight…" Princess Cadence said as she joined her on the floor once more, pointing at the empty pedestal right underneath the tapestry.

"You got it, Cadence…" Twilight smiled.

Captain Kirk approached Cadence. "I'd like to say something…"

"Yes?"

"To… every_pony…"_ he said as he glanced around the room.

Cadence smiled. "Certainly…" She then moved back up to the Throne's platform. "Everyone!" she called out as she raised a forehoof.

"Order! ORDER!" Flash Sentry called out, and everyone in the room immediately fell silent.

"Our friend, Captain James T. Kirk, has something he wishes to tell us all…" She then nodded to Kirk.

"Your Highnesses…" he began. "What you have done here today for me and my men is beyond _any _of our expectations. There is an old saying among my people: One good deed deserves another… In saying that, I would like to invite _all of you_ on board the Enterprise for a tour of our _wonderful _starship…"

Murmurs of surprise went up in the crowd. Captain Kirk's announcement was certainly a surprise! Dr. McCoy's facial expression and Mr. Spock's eyebrow raise certainly betrayed that same surprise.

"This invitation is also extended to Princess Twilight Sparkle and her brave friends…" Kirk continued. "You already know what the outside of our ship looks like…" he said as he gestured towards the Enterprise's image on the tapestry. "I think it's only fair that you see what the _inside _of our ship also looks like…"

The crowd continued to murmur in reaction to this announcement. They were quickly silenced as Princess Celestia came forward. "Captain James Tiberius Kirk, we would be _delighted…" _she said.

The crowd applauded at this decision.

As soon as the applause died down, Kirk spoke again. "Wonderful!" he said with a smile. "I'll make arrangements for this afternoon…"

Princess Celestia smiled and bowed.

With the ceremonies now over, Flash Sentry ushered everyone outside. Kirk and his men stopped briefly to admire the wonderful tapestry as they walked out.

"Captain…" Spock said as he joined Kirk outside in the hallway. "I presume it would be _pointless _of me to argue this decision you've just reached with you, knowing your usual _resolve…"_

Kirk nodded. "You'd be _right, _Mr. Spock. Bones?" He asked the good Doctor, who had also joined him.

"Well, I agree with Spock for once; and I know I'm not gonna change your mind, once it's made up, knowing you too well, Jim…"

"In any case, I do not have time to continue this discussion any further…" Spock continued. "I have a… _date… _with Rainbow Dash that I must keep…"

Kirk was surprised. "A _date, _Spock!?"

The Vulcan nodded. "I have decided to take up her challenge for a race she made with me exactly seven days ago…"

"Hey, Spock!" Rainbow Dash called as she came to stand next to the Vulcan. "Still on for that race later on?"

"Indeed I am…" Spock replied.

"You know, I don't think even a Vulcan like you can beat somepony as _awesome _as me!" Rainbow Dash boasted.

Spock raised an eyebrow. "We shall see…"

"Now _this _I have to witness!" McCoy said as Rainbow Dash trotted towards the banquet hall where a brunch buffet was being served.

"Me, too!" Kirk admitted with a smile.

After brunch, a large crowd gathered outside the northeastern part of the Imperial City. Most of the gathered crowd were crystal ponies curious to see the end result of a race between who was greatly considered to be the most awesome Pegasus in Equestria and an alien Vulcan from another world.

An aerial course was set up for this occasion that would have the racers navigate through a forest, a cloud slalom course and some mountains of the North Pole Barrier before reaching the finish line.

Since it was already established from their previous mission that Spock's projected bat pony form was capable of flying, it only made sense that the race challenge between them would be an aerial one. Spock himself explained this phenomenon as being due to the magical energy fields forever present on the planet that his bat pony guise was capable of flight.

They saw the two racers leave the starting line a half hour ago. Spock was given a thirty second lead, as promised by Rainbow Dash. Once the thirty seconds were up, Rainbow Dash took off like a rocket after Spock. Now, they were waiting for the victor to cross the finish line.

"Look!" a pony from the crowd exclaimed. "Somepony's coming…" She pointed.

"It's Rainbow Dash!" the female pony sitting next to her said.

Indeed, it _was _Rainbow Dash moving very fast and looking as confident as ever! Within moments, she was almost to the finish line. When she crossed it, she lifted her forehooves over her head as a sign of victory, then she skidded to a halt and settled softly to the ground. The entire crowd cheered her victory as her closest friends gathered around her to congratulate her.

"Another _outstandin' _race, Rainbow Dash!" Applejack said in congratulations.

"Of course…" Rainbow Dash said arrogantly as she pretended to shine her hoof on her chest.

"Where's Spock?" Twilight Sparkle asked as she looked out over the horizon.

"I don't know…" Rainbow Dash shrugged. "Last time I saw him was back at the entrance to the forest area, _eating my dust!"_

"Ya we're SUPPOSED ta give him a _head start!" _Applejack exclaimed.

"I waited thirty seconds!" Rainbow Dash countered.

"Maybe ya shoulda waited thirty _minutes…" _Applejack said sarcastically.

Rainbow Dash glared at her.

"OOH OOH OOH! There he is!" Pinkie Pie jumped up as she pointed.

Everybody looked and they did, in fact, see Spock's bat pony form approaching slowly from the northwest. As he grew nearer, everybody saw that he was looking really tired and the simple act of flying was a monumental effort for him.

The gathered crowd shouted encouragement at him as he neared the finish line. The crowd cheered as he crossed the finish line, immediately crashed to the ground and slid to a halt. He was breathing heavily from exhaustion as the crowd gathered around him.

"All right, everypony, _stand back! _Give him some air!" Captain Kirk said as he intervened and motioned the crowd back. "You ok, Spock?" Kirk asked as he crouched down beside the prone Vulcan.

"_Fine, _Captain…" Spock breathed.

"I guess no amount of Starfleet training is enough to beat a pony as _awesome _as Rainbow Dash…" Dr. McCoy jibed.

"I am inclined to _agree…" _Spock said, still trying to catch his breath.

When he finally did get up, the crowd erupted in cheers and applause. "That was _awesome!" _Rainbow Dash cried as she gave Spock a congratulatory hug.

"But you were _more _awesome today…" Spock said as he returned the hug.

At least there was no bad blood between them, and they still remained friends.

_Captain's Log, Supplemental – Having just been paid a high honour by Equestrian Royalty in the Imperial City of The Crystal Empire, I've decided to return the favour by inviting said Royalty aboard the Enterprise for a grand tour._

The doors to the Transporter Room SWISHed open to reveal Captain Kirk. Chief Engineer Scott was at the console. He had just beamed aboard Twilight Sparkle and her friends, and they were all patiently waiting in the Transporter Room for the Royals to arrive.

"Scotty…" Kirk said as he approached the Enterprise's Chief Engineer. "Looks like you've made a new _friend…" _He smiled as he saw that Twilight Sparkle was standing next to Scott behind the Transporter's console.

"Oh! Well, the purple lass here was curious about the functioning of the Transporter console, so I thought I'd _indulge _her."

"I just find equipment like this to be _fascinating!" _Twilight Sparkle said with a smile.

"Yeah! You'd expect that from an _egghead _like _her…" _Rainbow Dash said.

Applejack frowned as she poked the rainbow coloured Pegasus in the ribs. Rainbow Dash laughed nervously as she flashed a toothy smile.

"Do you have them?" Kirk asked Scotty.

"They're at the coordinates, sir. Ah can beam them up _anytime. _Just give tha word!" Scotty said.

"Energize, Mr. Scott!" Kirk ordered.

The Transporter console WHIRRed as Scotty pushed down on the energizer levers. The Transporter warbled as the forms of Princesses Celestia, Luna, Cadence and Prince Shining Armour materialized on the Transporter's platform.

"Welcome aboard the Enterprise, Your Highnesses!" Kirk said as he bowed.

Shining Armour checked himself to make sure he was still whole as the alicorn Royals stepped down off of the Transporter platform. He chuckled. "That Transporter thing really _works!" _he said.

"Why of COURSE it works, lad! Ah woulda beamed ya up in _pieces _if it _didn't!" _Scott told Shining Armour as he places his fists on his hips.

Shining Armour looked at Scotty with equine alarm in his eyes.

"You must forgive my Chief Engineer." Kirk told Shining Armour right away. "He's quite _touchy _when it comes to the ship's functions…"

Shining Armour smiled. "Of course, Captain!"

"Aye!" Scotty said. "Ah'm the reason everything on this vessel is ship shape! Why, they'd be _helpless _without me as their Chief Engineer…"

"I do not doubt that for a _minute, _Mr. Scott!" Princess Luna said.

"Well, now…" Kirk said. "If you'd all follow me, let's begin our grand tour of the ship…" he motioned for everypony to follow him through the double doors leading to the hallway.

"See ya all in Engineering later on!" Scotty cried as everyone filed out of the room.

The double doors SWISHed close once everyone had left the Transporter Room.

The doors to the Enterprise's Sick Bay SWISHed open to allow Captain Kirk and his tour group inside.

"I gotta say there's not a lot of room to _fly _on this ship…" Rainbow Dash said as she hovered in.

"Well, it wasn't _designed _for that…" Kirk said.

"Yeah! Pay attention, Dash!" Applejack said.

Rainbow Dash just glared at her.

Kirk waited until everyone entered the room before he spoke. "This is the Enterprise's Sick Bay where we treat our sick and wounded…"

"Is this where mah younger sister an 'er friends got treated fer that _disease?" _Applejack asked.

"That's _right." _Kirk said. "This was _also _where the cure for said disease was _patented. _And there's good 'ol Dr. McCoy hard at work!"

"Welcome to Sick Bay, everypony!" McCoy said as he approached the group. "I don't mean to be _boastful; _but if it weren't for _me, _they'd have _no idea_ how to run this place…" he smiled.

Nurse Chapel, who was at a nearby console, just shook her head at this.

Fluttershy came forward and looked around. "So this is where you spend most of your time, huh?" she asked.

"That's _right."_McCoy said. "When you're a _Doctor, _you sometimes have to work long hours. If you have time later, I can give you a _full physical…" _He told Fluttershy with a smile.

Fluttershy giggled. "Oh, _Doctor!" _She blushed as she waved a hoof at him.

Kirk turned to leave, but then remembered something. "_Oh, _Bones!…" Kirk began as he turned back to face McCoy. "I have some _very special _friends here to see you. They _insisted _upon beaming up to pay you a visit…"

"Oh? Who is it?" McCoy asked.

With this, three fillies galloped into Sick Bay. "HI, DOC!" they exclaimed in unison as they ran straight for McCoy.

"Well, I'll be _damned!" _McCoy exclaimed when he saw who it was.

It was Apple Bloom and her two friends Sweetie Belle and Scootaloo, the very same fillies Dr. McCoy cured from the new Vegan Chorial Meningitis strain just seven days ago.

"WHOA, don't bowl me _over!" _McCoy cried out as the three fillies crashed into him. They giggled as they embraced him.

While this was going on, an Ensign walked into Sick Bay and handed three black cases to Captain Kirk. "Ah! Right on time…" Kirk said as he accepted the boxes from the Ensign.

"Uhh… Excuse me… girls…" Kirk told the three fillies, who interrupted their revelry with Dr. McCoy to face the Captain of the Enterprise.

"I have something _very special _here for all three of you." Kirk said.

"What it is, Mr. Kirk?" Scootaloo asked.

"It's a replica of an ancient medal of honour among my people called the _Purple Heart."_

Kirk brought out one of the medals to show it to the girls.

"OOOOOOOHHH…" the three fillies said in unison in reaction to how beautiful it was.

"Historically, it was always given to someone among my people who showed _great courage and accomplishment _during battle. You three fillies showed _great courage _during the epidemic that plagued your people seven days ago, and it was thanks to _you three _that we were able to discover the _cure _against that disease. In other words, you've BATTLED the disease that plagued you; and if that, in itself, is not a great ACCOMPLISHMENT, I don't know what is."

As Kirk moved to place the gold plated medals tied to the purple coloured ribbon necklace around the fillies' necks, he said the following final phrase. "I personally can't think of _anyone else _more deserving of these medals than _you three!"_

All three fillies held up the medals they were just given to examine it.

"WOW!" Scootaloo exclaimed as she held up her medal.

"This is really GREAT!" Sweetie Belle said as she held up hers.

"Ah'm NEVER gonna lose THIS medal!" Apple Bloom said as she held up hers.

"Now isn't that a _great honour!?" _Applejack said proudly.

"It sure IS!" Apple Bloom said. "But… Who's this guy on the _front?"_ she questioned.

"Oh, that's _George Washington." _Kirk said in answer. "He was a _very important man _in our history. He was what is called a 'President', and he was the _very first one _of the country on our world known as the old _United States of America…"_

"So what do we _say, _girls!?" Applejack prompted.

"THANK YOU, MR. KIRK!" the three fillies exclaimed in unison.

Kirk smiled. "You're quite welcome!"

"Y'know, girls, ah've been thinkin' 'bout becomin' a _Doctor _when ah grow up." Apple Bloom said. "So whatdya think about a Doctor's _cutie mark, _Sweetie Belle?"

"I seriously _doubt _it, Apple Bloom!" Sweetie Belle said.

"Well, we could always try for that _space exploring _cutie mark again, girls!" Scootaloo said. "I still wanna try-"

Sweetie Belle used her unicorn magic to pull Scootaloo's face close to hers. "Don't even _think _about it, Scootaloo!" she said as she glared at the Pegasus filly, who smiled nervously.

Everyone in the room laughed at this exchange.

When the laughter died down, Kirk spoke again. _"Now,_ if you'll all follow me,let's continue with our _grand tour. _Next stop: Main Engineering! The virtual _heart and soul _of the ship!"

The double doors leading to the hallway SWISHed open to allow Captain Kirk to leave.

"That was a _real nice thing _ya've done for the girls…" Applejack told Kirk as they walked into the hallway. "Ya've just made three new friends _fer life!" _

"We aim to please…" Kirk said with a smile.

The group continued down the hallway towards Main Engineering. Apple Bloom and her friends were at the back of the group chatting away happily as they continued to admire the Purple Heart medals they were just given.

Later that day, the entire group was back in the Imperial City of the Crystal Empire gathered at the Imperial Square where the Crystal Heart was back on display. The Enterprise wasn't due to leave until a few hours, so they all decided to spend their last moments together on the planet. The Princesses and Shining Armour left to return to the palace, but Twilight Sparkle decided to stay with her friends. Spike had joined them, having arrived at the Crystal Empire only a few minutes ago.

"That was a most super duper luper FANTASTIC tour, wasn't it, girls!?" Pinkie Pie asked, still bouncing with excitement.

"It most _certainly _was!" Rarity said in answer.

"I was most impressed by the _Main Bridge…" _Twilight Sparkle admitted. "Seeing all those control panels, watching all of those people _work…"_

"You _would…" _Rainbow Dash with a roll of her eyes.

"Aw, come on, Rainbow Dash!" Applejack said. "There musta been _somethin' _ya liked 'bout that _tour?"_

"Well… The Shuttle Bay was pretty neat… At least you had room to _fly _in there."

Applejack sighed. "Ya ain't never gonna _change, _are ya, Rainbow?"

The rainbow coloured Pegasus just smiled and shrugged.

"Well, I know I really liked the _Sick Bay…" _Fluttershy said softly.

"Oh, PLEASE! The only reason you liked the Sick Bay was because Dr. McCoy was there!" Rarity said.

"Oh, _no!" _Fluttershy said, shaking her head. "It was because… Okay, it WAS because Dr. McCoy was there." She admitted as she patted the Doctor's hand, which rested lovingly on her back.

"Well, _I, _for one, wouldn't be caught _dead _in a place like that!" the white unicorn said as she fluffed her mane.

"Tha only tahm ya'd be in there is if ya WE'RE dead, Rarity!" Applejack said sarcastically.

Rarity ignored her, however, and turned her attention to Captain Kirk. "So I guess this is _goodbye, _isn't it?" She looked up at him sadly.

Kirk pursed his lips. "Not necessarily. It's true that we have to report to Star Base 9 because some of our crew is to be reassigned; but all of the Senior Staff, myself included, are due to have two months' worth of shore leave while the Enterprise undergoes resupply and maintenance; and I see no reason why we can't spend it _here…" _He smiled down at Rarity.

Rarity smiled lovingly back up at him.

"But… how can you get back here without your _ship?" _Fluttershy asked.

"Well, with fourteen other vessels like it in the Fleet, we can always ask another starship to drop us off… The U.S.S. Potempkin, for example! Captain Michael Fisher owes me a _big favour."_

"But you owe big favours to _everyone else, _Jim! Including _me…" _Dr. McCoy said.

"In due time, Bones…" Kirk told him.

"So are you gonna come back and spend your shore leave time with _me, _Doctor?" Fluttershy asked McCoy hopefully.

Dr. McCoy bent down to face her. "You know I will, Fluttershy. You can call me _Leonard, _you know."

"I'll look forward to it… _Leonard." _Fluttershy said with a soft smile.

McCoy then reached over and kissed Fluttershy on the cheek. Then they both embraced, Fluttershy humming softly as she still savoured that kiss.

"So are you gonna come back to spend some time with me, Chekhov!?" asked a still bouncing Pinkie Pie.

"Of course!" answered the Enterprise's Russian Navigator.

"YIPEEEEEEE!" exclaimed Pinkie Pie as she bounced around in excitement. "I'll be SOOOO looking forward to it! Wecangoforpinicsintheparktryoutnewandexcitingbakin grecipesetogetherI can'tWAITtotakeyoutoSugarcubeCornerwherewecan-"

Chekhov surprised the bouncing pink coloured Earth pony by grabbing her face and pressing his lips against hers in a kiss. When Chekhov released the kiss, Pinkie Pie was speechless as she maintained that look of equine surprise. Her look of shock quickly turned to infatuation as she smiled lovingly at the young Ensign Navigator. She sighed contently as she took Chekhov into her forelegs in a loving embrace.

Chekhov smiled and sighed. "Works every time…" he said over her shoulder as he wrapped his arms around Pinkie Pie.

"Well, Mr. Kirk…" Rarity began.

"You can call me _Jim, _you know." Kirk told her.

Rarity smiled back. "Well, _Jim… _Since we still have a few hours to go before you leave, perhaps you would care for a little tour of the downtown area?" She fluffed her mane. "I can show all of the _hot spots, _and everything…"

"I'd be _delighted!" _Kirk said as he stuck his arm out for Rarity to grab with her forehoof, which she did.

Spike grumbled angrily. "I _hate _him!" he growled as he crossed his arms.

Twilight Sparkle giggled. "Oh, Spike!"

"You're all more than welcome to _join _us, of course!" Rarity said over her shoulder to all those assembled.

"I think we _will!" _Dr. McCoy said.

"Come along, Spike." Twilight Sparkle said as she moved to follow the group.

"Humpf!" Spike said as he followed Twilight Sparkle, still looking angry and keeping his arms crossed.

The merry bunch of humans and ponies made their way to the downtown area. The couples Kirk and Rarity, as well as McCoy and Fluttershy, were walking along arm in foreleg; while Chekhov kept his hand on Pinkie Pie's back as she bounced along beside him.

A few hours later, at dusk, they all said their goodbyes and promised to meet each other again in seven days' time in Ponyville where Kirk and his friends are to begin their shore leave.

The Enterprise left orbit a short time after Kirk and his friends beamed back up, and set a course for Star Base 9.


End file.
